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.

1

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

3

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

4

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

5

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

6

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

7

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

10

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

11

HO4 0.399H5 0.018H6A 0.061H6B 0.061

12

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

14

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

16

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

18

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

19

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

21

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

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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