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SI Tables
Table S1. Protonation states calculated using the Mn-depleted PSII structure (PDB codes 5MX2) 2.
residue protonation [H+]ligandD1-Asp170 1.0D1-Glu189 1.0D1-His332 1.0D1-Glu333 1.0D1-Asp342 0.0 aD1-Ala344 b 1.0CP43-Glu354 1.0
H-bond partnerD1-His337 1.0
a D1-Asp342 was ionized but it accepted H-bonds from protonated D1-Glu189 and protonated D1-His337. b The carboxy terminus of the D1 protein.
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Electronic Supplementary Material (ESI) for Chemical Science.This journal is © The Royal Society of Chemistry 2018
Table S2. Atomic partial charges of Chla and Pheoa. –, not applicable.
Chla•+ Chla Chla•− Pheoa Pheoa•−
MG 0.878 0.821 0.747 – –CHA 0.086 0.071 0.081 0.109 0.081CHB -0.386 -0.365 -0.350 -0.337 -0.360HHB 0.161 0.144 0.129 0.144 0.135CHC -0.255 -0.221 -0.247 -0.161 -0.205HHC 0.146 0.138 0.131 0.127 0.118CHD -0.359 -0.280 -0.326 -0.220 -0.296HHD 0.189 0.173 0.169 0.165 0.165NA -0.345 -0.311 -0.302 -0.241 -0.247C1A 0.043 -0.008 -0.062 -0.081 -0.133C2A 0.081 0.062 0.074 0.217 0.255H2A 0.061 0.050 0.040 0.023 0.011C3A 0.061 0.080 0.076 0.174 0.190H3A 0.072 0.050 0.033 0.006 -0.021C4A 0.318 0.233 0.180 0.153 0.100CMA -0.419 -0.457 -0.479 -0.418 -0.373HMA1 0.128 0.126 0.123 0.105 0.082HMA2 0.128 0.126 0.123 0.105 0.082HMA3 0.128 0.126 0.123 0.105 0.082CAA -0.051 0.028 0.074 -0.037 0.025HAA1 0.040 0.003 -0.024 0.040 0.019HAA2 0.040 0.003 -0.024 0.040 0.019CBA -0.296 -0.302 -0.301 -0.548 -0.578HBA1 0.069 0.073 0.077 0.144 0.136HBA2 0.069 0.073 0.077 0.144 0.136CGA 0.787 0.788 0.787 0.856 0.875O1A -0.512 -0.526 -0.538 -0.529 -0.536O2A -0.404 -0.407 -0.407 -0.413 -0.418NB -0.436 -0.371 -0.285 -0.115 -0.044HNB – – – 0.189 0.170C1B 0.223 0.131 0.014 0.087 0.007C2B 0.132 0.151 0.156 0.123 0.115C3B -0.071 -0.088 -0.156 -0.063 -0.130C4B 0.248 0.135 0.086 0.039 -0.001CMB -0.376 -0.350 -0.278 -0.311 -0.248HMB1 0.128 0.105 0.071 0.100 0.070HMB2 0.128 0.105 0.071 0.100 0.070HMB3 0.128 0.105 0.071 0.100 0.070CAB -0.077 -0.045 0.006 -0.051 0.000HAB 0.122 0.105 0.087 0.112 0.096CBB -0.331 -0.391 -0.475 -0.387 -0.474HBB1 0.174 0.163 0.147 0.164 0.148
2
HBB2 0.174 0.163 0.147 0.164 0.148NC -0.458 -0.381 -0.348 -0.292 -0.298C1C 0.193 0.091 0.040 0.065 0.040C2C 0.140 0.141 0.147 0.138 0.137C3C -0.221 -0.234 -0.229 -0.246 -0.248C4C 0.360 0.221 0.183 0.201 0.195CMC -0.356 -0.328 -0.331 -0.329 -0.320HMC1 0.125 0.100 0.087 0.100 0.085HMC2 0.125 0.100 0.087 0.100 0.085HMC3 0.125 0.100 0.087 0.100 0.085CAC 0.062 0.143 0.206 0.157 0.210HAC1 0.039 0.000 -0.036 -0.006 -0.036HAC2 0.039 0.000 -0.036 -0.006 -0.036CBC -0.186 -0.197 -0.182 -0.178 -0.185HBC1 0.064 0.053 0.036 0.046 0.037HBC2 0.064 0.053 0.036 0.046 0.037HBC3 0.064 0.053 0.036 0.046 0.037ND -0.470 -0.395 -0.339 -0.027 0.009HND – – – 0.091 0.072C1D 0.288 0.143 0.094 0.005 -0.013C2D 0.114 0.113 0.089 0.171 0.118C3D -0.196 -0.218 -0.269 -0.272 -0.301C4D 0.188 0.124 0.088 0.037 0.028CMD -0.345 -0.300 -0.233 -0.320 -0.254HMD1 0.129 0.098 0.061 0.105 0.071HMD2 0.129 0.098 0.061 0.105 0.071HMD3 0.129 0.098 0.061 0.105 0.071CAD 0.629 0.627 0.618 0.661 0.641OBD -0.424 -0.473 -0.535 -0.481 -0.542CBD -0.624 -0.630 -0.653 -0.618 -0.642HBD 0.217 0.207 0.197 0.213 0.207CGD 0.840 0.859 0.870 0.763 0.786O1D -0.529 -0.536 -0.547 -0.508 -0.536O2D -0.379 -0.398 -0.407 -0.338 -0.342CED 0.032 0.068 0.106 0.019 0.064HED1 0.076 0.055 0.032 0.067 0.044HED2 0.076 0.055 0.032 0.067 0.044HED3 0.076 0.055 0.032 0.067 0.044C1 0.083 0.094 0.109 0.103 0.102H1 0.079 0.066 0.052 0.060 0.046H2 0.079 0.066 0.052 0.060 0.046
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Table S3. Atomic partial charges of BChla and BPheoa. –, not applicable.
BChla•+ BChla BChla•− BPheoa BPheoa•−
MG 0.872 0.816 0.763 – –CHA 0.100 0.089 0.097 0.150 0.117CHB -0.410 -0.378 -0.408 -0.400 -0.448HHB 0.157 0.144 0.135 0.151 0.143CHC -0.444 -0.389 -0.429 -0.387 -0.426HHC 0.201 0.180 0.172 0.180 0.170CHD -0.445 -0.404 -0.396 -0.364 -0.412HHD 0.185 0.169 0.151 0.168 0.158NA -0.243 -0.203 -0.218 -0.230 -0.265C1A -0.025 -0.085 -0.130 -0.047 -0.056C2A -0.066 -0.043 -0.051 -0.051 -0.078H2A 0.100 0.087 0.083 0.080 0.082C3A 0.247 0.273 0.295 0.232 0.264H3A 0.019 -0.007 -0.029 -0.009 -0.034C4A 0.189 0.090 0.060 0.178 0.164CMA -0.429 -0.412 -0.401 -0.384 -0.367HMA1 0.126 0.108 0.095 0.100 0.085HMA2 0.126 0.108 0.095 0.100 0.085HMA3 0.126 0.108 0.095 0.100 0.085CAA -0.042 -0.016 0.094 0.021 0.099HAA1 0.069 0.058 0.025 0.044 0.023HAA2 0.069 0.058 0.025 0.044 0.023CBA -0.410 -0.437 -0.488 -0.442 -0.497HBA1 0.132 0.130 0.132 0.129 0.133HBA2 0.132 0.130 0.132 0.129 0.133CGA 0.755 0.735 0.721 0.743 0.738O1A -0.506 -0.479 -0.473 -0.486 -0.473O2A -0.379 -0.382 -0.379 -0.385 -0.389NB -0.524 -0.453 -0.419 -0.232 -0.200HNB – – – 0.209 0.205C1B 0.299 0.193 0.152 0.161 0.129C2B 0.164 0.174 0.140 0.161 0.116C3B -0.374 -0.432 -0.510 -0.428 -0.499C4B 0.438 0.350 0.355 0.298 0.292CMB -0.352 -0.319 -0.253 -0.299 -0.222HMB1 0.122 0.096 0.063 0.095 0.059HMB2 0.122 0.096 0.063 0.095 0.059HMB3 0.122 0.096 0.063 0.095 0.059CAB 0.686 0.715 0.735 0.726 0.741CBB -0.509 -0.518 -0.524 -0.532 -0.535HBB1 0.150 0.136 0.121 0.141 0.124HBB2 0.150 0.136 0.121 0.141 0.124
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HBB3 0.150 0.136 0.121 0.141 0.124OBB -0.469 -0.508 -0.563 -0.504 -0.561NC -0.307 -0.235 -0.244 -0.213 -0.243C1C 0.190 0.058 0.035 0.102 0.071C2C 0.198 0.282 0.293 0.265 0.314H2C 0.026 -0.010 -0.017 -0.008 -0.029C3C -0.033 -0.016 -0.055 -0.073 -0.086H3C 0.064 0.037 0.034 0.046 0.030C4C 0.232 0.116 0.081 0.148 0.141CMC -0.303 -0.295 -0.291 -0.297 -0.278HMC1 0.090 0.072 0.062 0.073 0.056HMC2 0.090 0.072 0.062 0.073 0.056HMC3 0.090 0.072 0.062 0.073 0.056CAC -0.028 -0.015 0.006 0.020 0.032HAC1 0.036 0.025 0.023 0.016 0.012HAC2 0.036 0.025 0.023 0.016 0.012CBC -0.185 -0.180 -0.196 -0.190 -0.190HBC1 0.063 0.047 0.040 0.049 0.036HBC2 0.063 0.047 0.040 0.049 0.036HBC3 0.063 0.047 0.040 0.049 0.036ND -0.513 -0.462 -0.403 -0.092 -0.060HND – – – 0.104 0.089C1D 0.372 0.261 0.177 0.140 0.108C2D 0.077 0.080 0.062 0.090 0.053C3D -0.181 -0.242 -0.298 -0.233 -0.300C4D 0.171 0.136 0.116 0.017 0.026CMD -0.311 -0.288 -0.228 -0.271 -0.204HMD1 0.122 0.097 0.062 0.095 0.060HMD2 0.122 0.097 0.062 0.095 0.060HMD3 0.122 0.097 0.062 0.095 0.060CAD 0.612 0.651 0.666 0.667 0.687OBD -0.425 -0.481 -0.543 -0.479 -0.544CBD -0.589 -0.600 -0.680 -0.636 -0.679HBD 0.213 0.188 0.196 0.198 0.191CGD 0.832 0.823 0.852 0.839 0.844O1D -0.529 -0.525 -0.538 -0.528 -0.536O2D -0.350 -0.370 -0.386 -0.365 -0.381CED -0.006 0.063 0.080 0.029 0.068HED1 0.081 0.051 0.037 0.060 0.040HED2 0.081 0.051 0.037 0.060 0.040HED3 0.081 0.051 0.037 0.060 0.040C1 0.092 0.081 0.055 0.081 0.076H1A 0.080 0.073 0.072 0.072 0.064H1B 0.080 0.073 0.072 0.072 0.064
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Table S4. Atomic partial charges of ubiquinone (UQ).
UQ UQ•−
C1 -0.008 -0.039C1M -0.240 -0.090H1MA 0.090 0.018H1MB 0.090 0.018H1MC 0.090 0.018C2 0.430 0.228O2 -0.401 -0.476C3 0.115 0.078O3 -0.237 -0.312C3M 0.027 0.104H3MA 0.059 0.010H3MB 0.059 0.010H3MC 0.059 0.010C4 -0.065 0.032O4 -0.259 -0.310C4M 0.051 0.131H4MA 0.048 0.002H4MB 0.048 0.002H4MC 0.048 0.002C5 0.477 0.297O5 -0.350 -0.464C6 -0.254 -0.253C7 0.145 0.254H7A 0.028 -0.031H7B 0.028 -0.031C8 -0.377 -0.373H8 0.144 0.125C9 0.249 0.224C10 -0.314 -0.290H10A 0.089 0.066H10B 0.089 0.066H10C 0.089 0.066C11 -0.225 -0.224H11A 0.089 0.066H11B 0.089 0.066
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Table S5. Atomic partial charges of plastoquinone (PLQ).
PLQ PLQ•−
C2 -0.352 -0.402C3 -0.082 -0.171C4 0.480 0.324C5 -0.067 -0.084C6 -0.103 -0.122C1 0.558 0.442C7 0.264 0.448C8 -0.467 -0.487C9 0.294 0.243C10 -0.373 -0.336C11 -0.268 -0.254C52 -0.130 -0.099C53 -0.152 -0.053O1 -0.437 -0.557O2 -0.427 -0.575H2 0.160 0.139H7A 0.007 -0.061H7B 0.007 -0.061H8 0.163 0.165H10A 0.106 0.081H10B 0.106 0.081H10C 0.106 0.081H11A 0.104 0.081H11B 0.104 0.081H52A 0.065 0.023H52B 0.065 0.023H52C 0.065 0.023H53A 0.068 0.009H53B 0.068 0.009H53C 0.068 0.009
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Table S6. Atomic partial charges of spheroidene.
spheroideneCM1 0.145HM1A 0.015HM1B 0.015HM1C 0.015O1 -0.462C1 0.655C2 -0.407H2A 0.093H2B 0.093H2C 0.093C3 -0.407H3A 0.093H3B 0.093H3C 0.093C4 -0.314H4A 0.089H4B 0.089C5 0.014H5 0.095C6 -0.330H6 0.137C7 0.221C8 -0.265H8A 0.078H8B 0.078H8C 0.078C9 -0.286H9 0.136C10 -0.006H10 0.116C11 -0.283H11 0.141C12 0.185C13 -0.245H13A 0.075H13B 0.075H13C 0.075C14 -0.254H14 0.124C15 -0.045H15 0.132
8
C16 -0.250H16 0.149C17 0.209C18 -0.336H18A 0.095H18B 0.095H18C 0.095C19 -0.259H19 0.130C20 -0.102H20 0.121C21 -0.078H21 0.125C22 -0.264H22 0.127C23 0.214C24 -0.243H24A 0.073H24B 0.073H24C 0.073C25 -0.317H25 0.141C26 0.014H26 0.122C27 -0.285H27 0.144C28 0.061C29 -0.255H29A 0.083H29B 0.083H29C 0.083C30 -0.114H30A 0.050H30B 0.050C31 0.215H31A 0.000H31B 0.000C32 -0.399H32 0.135C33 0.099C34 -0.286H34A 0.088H34B 0.088H34C 0.088C35 -0.132
9
H35A 0.051H35B 0.051C36 0.244H36A 0.000H36B 0.000C37 -0.518H37 0.159C38 0.309C39 -0.368H39A 0.100H39B 0.100H39C 0.100C40 -0.368H40A 0.100H40B 0.100H40C 0.100
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Table S7. Atomic partial charges of sulfoquinovosyl diacylglycerol (SQD).
SQD−
O6 -0.398C44 0.077C45 0.235C46 0.152O47 -0.359C7 0.735O49 -0.540C8 -0.302O48 -0.388C23 0.788O10 -0.546C24 -0.358C1 0.428C2 0.114O2 -0.601C3 0.202O3 -0.628C4 0.041O4 -0.606C5 0.312C6 -0.221O5 -0.433S 1.004O7 -0.610O8 -0.610O9 -0.610H44A 0.062H44B 0.062H45 0.020H46A 0.000H46B 0.000H8A 0.117H8B 0.117H24A 0.136H24B 0.136H1 0.003H2 0.062HO 0.398H3 0.022HO3 0.412H4 0.036
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HO4 0.399H5 0.018H6A 0.061H6B 0.061
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Table S8. Atomic partial charges of heptyl 1-thiohexopyranoside (HTG).
HTGC1 0.039S1 -0.219C2 0.274O2 -0.609C3 0.072O3 -0.618C4 0.145O4 -0.601C5 0.361O5 -0.415C6 0.064O6 -0.600C1' 0.008C2' -0.015C3' 0.098C4' -0.175C5' -0.047C6' 0.139C7' -0.275H1 0.112H2 0.062HO 0.416H3 0.054HO3 0.426H4 0.042HO4 0.393H5 -0.038H6A 0.036H6B 0.036HO6 0.410H1'1 0.062H1'2 0.062H2'1 0.002H2'2 0.002H3'1 -0.002H3'2 -0.002H4'1 0.044H4'2 0.044H5'1 0.021H5'2 0.021H6'1 -0.009
13
H6'2 -0.009H7'1 0.063H7'2 0.063H7'3 0.063
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Table S9. Atomic partial charges of the Fe complex in PbRC.
Fe complex (PbRC)1FE 0.746
Glu-M2342CB -0.0812HB1 0.0362HB2 0.0362CG 0.0342HG1 0.0052HG2 0.0052CD 0.6332OE1 -0.6352OE2 -0.635His-L1903CB -0.2583HB1 0.1263HB2 0.1263CG 0.2683ND1 -0.3003HD1 0.3403CD2 -0.2543HD2 0.1683CE1 0.0383HE1 0.1563NE2 -0.197His-M2194CB -0.2584HB1 0.1264HB2 0.1264CG 0.2684ND1 -0.3004HD1 0.3404CD2 -0.2544HD2 0.1684CE1 0.0384HE1 0.1564NE2 -0.197His-M2665CB -0.2585HB1 0.1275HB2 0.1275CG 0.2685ND1 -0.300
15
5HD1 0.3405CD2 -0.2545HD2 0.1685CE1 0.0385HE1 0.1565NE2 -0.197His-L1906CB -0.2586HB1 0.1276HB2 0.1276CG 0.2686ND1 -0.3006HD1 0.3406CD2 -0.2546HD2 0.1686CE1 0.0386HE1 0.1566NE2 -0.197
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Table S10. Atomic partial charges of the Fe complex in PSII.
Fe complex (PSII)1FE 0.695
HCO3−
2C 0.8472O1 -0.5342O2 -0.6352O3 -0.6352HO 0.385D2-His2143CB -0.2593CG 0.2663ND1 -0.2883CD2 -0.2623CE1 0.0373NE2 -0.1823HB1 0.1313HB2 0.1313HD1 0.3423HD2 0.1743HE1 0.153D1-His2154CB -0.2714CG 0.3284ND1 -0.3304CD2 -0.3564CE1 0.0094NE2 -0.0904HB1 0.1304HB2 0.1304HD1 0.3474HD2 0.1884HE1 0.181D1-His2725CB -0.2585CG 0.2095ND1 -0.2325CD2 -0.1765CE1 -0.0295NE2 -0.2395HB1 0.1285HB2 0.1285HD1 0.324
17
5HD2 0.1515HE1 0.178D2-His2686CB -0.2706CG 0.2736ND1 -0.3366CD2 -0.2296CE1 0.1146NE2 -0.2526HB1 0.1306HB2 0.1306HD1 0.3466HD2 0.1596HE1 0.119
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Table S11. Atomic partial charges of the Mn4CaO5 cluster in S1.
Mn4CaO5 cluster1Mn1 1.3981Mn2 1.7681Mn3 1.9041Mn4 1.5491Ca1 1.7431O1 -1.0101O2 -1.1481O3 -0.9791O4 -1.0141O5 -1.071water ligand1OH1 -0.9351H11 0.4821H12 0.4501OH2 -0.9581H21 0.4441H22 0.5111OH3 -0.8621H31 0.4901H32 0.4961OH4 -0.9211H41 0.4581H42 0.536D1-Asp1702CB -0.3072CG 0.9322OD1 -0.8392OD2 -0.7952HB1 0.0912HB2 0.091D1-Glu1893CB -0.2923CG -0.0413CD 0.7573OE1 -0.6963OE2 -0.7153HB1 0.0853HB2 0.0853HG1 0.0813HG2 0.081D1-His332
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4ND1 -0.2944CG 0.4004CB -0.5154NE2 -0.1654CD2 -0.2944CE1 0.0294HD1 0.4354HB1 0.2134HB2 0.2134HD2 0.1744HE1 0.201D1-Glu3335CB -0.0845CG -0.0765CD 0.7845OE1 -0.6585OE2 -0.6525HB1 0.0645HB2 0.0645HG1 0.0455HG2 0.045D1-Asp3426CB -0.4166CG 0.9276OD1 -0.7376OD2 -0.7806HB1 0.1926HB2 0.192D1-Ala3447N -0.3107HN 0.3107CA -0.0167C 0.6587OT1 -0.6347CB -0.3137OT2 -0.6807HA 0.0547HB1 0.0997HB2 0.0997HB3 0.099CP43-Glu3548CB -0.1328CG -0.1858CD 0.8218OE1 -0.645
20
8OE2 -0.7488HB1 0.0568HB2 0.0568HG1 0.1138HG2 0.113CP43-Arg3579CB -0.2389CG -0.0339CD 0.3069NE -0.7099CZ 0.9119NH1 -0.8389NH2 -1.0079HB1 0.0959HB2 0.0959HG1 0.0419HG2 0.0419HD1 -0.0039HD2 -0.0039HE 0.4199HH11 0.4439HH12 0.4439HH21 0.5339HH22 0.533
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SI Figure legends
Figure S1. Em for one-electron reduction calculated using a) the cyanobacterial PSI crystal structure
(PDB code 1JB0) 3 and b) the plant PSI crystal structure (PDB code 4XK8) 4 in mV.
Figure S2. Em for one-electron reduction calculated using the crystal structures of PbRC from a)
Rhodobacter sphaeroides (PDB codes 1M3X) 5 and b) Thermochromatium tepidum (PDB codes 1EYS)
6 in mV.
Figure S3. (a) The binding interface of cytochrome c2 with PbRC 7 and (b) the corresponding region in
D1 (yellow) and D2 (blue) of PSII.
Figure S4. Em for one-electron reduction calculated using a) the 1.87 Å-structure (PDB codes 2J8C) 8
and b) the refined 1.87 Å-structure, where the methyl-keto O and C atoms in PM, BL, BM, HL, and HM in
the original 1.87 Å-structure were swapped.
Figure S5. Localization of hydrophobic residues (white sphere) and cofactors, spheroidene (red sphere)
and QB (cyan sphere), at the BM binding moiety. Hydrophobic residues shown are Trp-M66, Phe-M67,
Phe-M68, Phe-M74, Trp-M75, Phe-M85, Phe-M105, Trp-M115, Phe-M120, Phe-M123, Trp-M157,
Phe-M162, Trp-M171, Pro-M176, Tyr-M177, and His-M182.
Figure S6. a) Deletion of the QB isoprene side-chain from C56 to C16 in the 2.01 Å-PbRC crystal
structure (PDB code 3I4D) and b) changes in Em for one-electron reduction (red arrow) in mV. Note
that the QB isoprene side-chain is comprised of C16 in the 1.87 Å-PbRC crystal structure (PDB code
2J8C).
Figure S7. Loop a-b and helix cd of D2 in PSII (green) and subunit M in PbRC (cyan). The region
between D2-Val55 and Ser66 in PSII (red dotted circle), where D2-His61 9 is also located, is
structurally absent in PbRC.
22
Figure S8. Em for one-electron reduction calculated using the Mn-depleted PSII crystal structure (PDB
codes 5MX2) 2 in mV.
Figure S9. The amino acid sequences of the L and M subunits in PbRC and the D1 and D2 subunits in
PSII. Asp-M184, D1-Asn181/D2-Arg180, and Phe-L181/Tyr-M210 are in bold.
23
-1400
-1300
-1200
-1100
-1000
-900
A−1B A−1A
−1170−1188A0B A0A
−1088−1088
PAPB −1306
−1257
Em
(mV
)
-1300
-1200
-1100
-1000
-900
A−1B A−1A
−1173−1169
A0B A0A
−1049−1052
PA
PB −1264−1206
Em
(mV
)
a) cyanobacterial PSI b) plant PSI
Figure S1. Em for one-electron reduction calculated using a) the cyanobacterial PSI crystal structure
(PDB code 1JB0) 3 and b) the plant PSI crystal structure (PDB code 4XK8) 4.
24
Em
(mV
)
-1000
-900
-800
-700
-600
-500
-400
-300
−414
BL
−812
−945
HM HL−438
PM PL
−867−893
BM-1000
-900
-800
-700
-600
-500
-400
-300
−390
BM
BL
−774
−867
HM
HL−481
PMPL
−828−859
Em
(mV
)
a) PbRC (PDB code 1M3X) b) PbRC (PDB code 1EYS)
Figure S2. Em for one-electron reduction calculated using the crystal structures of PbRC from a)
Rhodobacter sphaeroides (PDB codes 1M3X) 5 and b) Thermochromatium tepidum (PDB codes 1EYS)
6.
25
spheroidene
cytochrome c2
Asp-L155
BA
Asp-M184
Lys-C97
Lys-C103
Glu-M95BB
a)
ChlD1
D2-His61
ChlD2
b)
D2D1
D1-Asn181D2-Arg180
D1-Asn181
ChlD1
D2-His61
ChlD2
D2-Arg180
c)
D2D1
cytochrome c2
Figure S3. (a) The binding interface of cytochrome c2 with PbRC (cyan) 7, (b) the corresponding region
in D1 (yellow) and D2 (blue) (where cytochrome c2 would exist) in PSII (green), and (c) comparison
between PbRC (cytochrome c2) and PSII (D1 and D2 proteins).
26
-1000
-900
-800
-700
-600
-500
-400
-300
-1000
-900
-800
-700
-600
-500
-400
-300
−400
BM
BL
−844
−965
HM
HL−486
PMPL
−852−839
−418
BL
−806
−915
HM
HL−475
PMPL
−888−877
BM
Em
(mV
)
Em
(mV
)
a) original 1.87 Å-structure (PDB code 2J8C)
b) refined 1.87 Å-structure
Figure S4. Em for one-electron reduction calculated using a) the 1.87 Å-structure (PDB codes 2J8C) 8
and b) the refined 1.87 Å-structure, where the methyl-keto O and C atoms in PM, BL, BM, HL, and HM in
the original 1.87 Å-structure were swapped.
27
Glu-M95 Asp-M184Asp-M173
BL
BM
PLPM
QB
spheroidene
Asp-L155
Figure S5. Localization of hydrophobic residues (white sphere) and cofactors, spheroidene (red sphere)
and QB (cyan sphere), at the BM binding moiety. Hydrophobic residues shown are Trp-M66, Phe-M67,
Phe-M68, Phe-M74, Trp-M75, Phe-M85, Phe-M105, Trp-M115, Phe-M120, Phe-M123, Trp-M157,
Phe-M162, Trp-M171, Pro-M176, Tyr-M177, and His-M182.
28
Figure S6. a) Deletion of the QB isoprene side-chain from C56 to C16 in the 2.01 Å-PbRC crystal
structure (PDB code 3I4D) and b) changes in Em for one-electron reduction (red arrow) in mV. Note
that the QB isoprene side-chain is comprised of C16 in the 1.87 Å-PbRC crystal structure (PDB code
2J8C).
29
TyrD…D2-His189
D2-Arg180
helix cd
D2-His61
D2-Val55–Ser66
loop a-b
Figure S7. Loop a-b and helix cd of D2 in PSII (green) and subunit M in PbRC (cyan). The region
between D2-Val55 and Ser66 in PSII (red dotted circle), where D2-His61 9 is also located, is
structurally absent in PbRC.
30
-1000
-900
-800
-700
-600
-500
-400
Em
(mV
)
ChlD2
ChlD1
−974
−863
PheoD2
PheoD1
−497
−606
PD1
PD2
−1000
−841
Figure S8. Em for one-electron reduction calculated using the Mn-depleted PSII crystal structure (PDB
codes 5MX2) 2 in mV.
31
Asp-M184,D1-Asn181/D2-Arg180↓ ↓Phe-L181/Tyr-M210
L-R.sphaeroides ayltlvlfrpvmmgawgyafpygiwthldwvsntgytygnfhynpahmiaisffftnalaL-T.tepidum aylvlvfvrpllmgawghgfpygilshldwvsnvgyqflhfhynpahmlaisffftnclaL-B.viridis mfcvlqvfrplllgswghafpygilshldwvnnfgyqylnwhynpghmssvsflfvnamaM-R.sphaeroides lwmvlgfirpilmgswseavpygifshldwtnnfslvhgnlfynpfhglsiaflygsallM-T.tepidum fylvlgfirpvmmgswakavpfgifphldwtaafsirygnlyynpfhmlsiaflygsallM-B.viridis fvlcigcihptlvgswsegvpfgiwphidwltafsirygnfyycpwhgfsigfaygcgllD1-T.elongatus safavfliypigqgsfsdgmplgisgtfnfmivfq-aehnilmhpfhqlgvagvfggalfD1-C.caldarium aatavfiiypigqgsfsdgmplgisgtfnfmlvfq-aehnilmhpfhmmgvagvfggslfD1-C.reinhardtii aasavflvypigqgsfsdgmplgisgtfnfmivfq-aehnilmhpfhmlgvagvfggslfD1-spinach aatavfliypigqgsfsdgmplgisgtfnfmivfq-aehnilmhpfhmlgvagvfggslfD2-T.elongatus vfvsvfliyplgqsswffapsfgvaaifrfllffq-gfhnwtlnpfhmmgvagvlggallD2-C.caldarium vfvsvfliyplgqaswffapsfgvaaifrfilflq-gfhnwtlnpfhmmgvagilggallD2-C.reinhardtii vfvsvfliyplgqsgwffapsfgvaaifrfilffq-gfhnwtlnpfhmmgvagvlgaallD2-spinach vfvsvfliyplgqsgwffapsfgvaaifrfilffq-gfhnwtlnpfhmmgvagvlgaall
: . * ..: . *: : : : * * .:. :
Figure S9. The amino acid sequences of the L and M subunits in PbRC and the D1 and D2 subunits in
PSII. Asp-M184, D1-Asn181/D2-Arg180, and Phe-L181/Tyr-M210 are in bold. Asterisks (*) indicate a
fully conserved site. Colons (:) indicate conservation between groups of strongly similar properties.
Dots (.) indicate conservation between groups of weakly similar properties.
32
SI References
1. Y. Umena, K. Kawakami, J.-R. Shen and N. Kamiya, Nature, 2011, 473, 55-60.2. M. Zhang, M. Bommer, R. Chatterjee, R. Hussein, J. Yano, H. Dau, J. Kern, H. Dobbek and A.
Zouni, eLife, 2017, 6, e26933.3. P. Jordan, P. Fromme, H. T. Witt, O. Klukas, W. Saenger and N. Krauss, Nature, 2001, 411,
909-917.4. X. Qin, M. Suga, T. Kuang and J. R. Shen, Science, 2015, 348, 989-995.5. A. Camara-Artigas, D. Brune and J. P. Allen, Proc. Natl. Acad. Sci. USA, 2002, 99, 11055-
11060.6. T. Nogi, I. Fathir, M. Kobayashi, T. Nozawa and K. Miki, Proc Natl Acad Sci U S A, 2000, 97,
13561-13566.7. H. L. Axelrod, E. C. Abresch, M. Y. Okamura, A. P. Yeh, D. C. Rees and G. Feher, J. Mol. Biol.,
2002, 319, 501-515.8. J. Koepke, E. M. Krammer, A. R. Klingen, P. Sebban, G. M. Ullmann and G. Fritzsch, J Mol
Biol, 2007, 371, 396-409.9. K. Saito, A. W. Rutherford and H. Ishikita, Proc Natl Acad Sci U S A, 2013, 110, 7690-7695.
33
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