7WFD: Photosystem I P700 chlorophyll a apoprotein A1
Left PSI in the cyclic electron transport supercomplex NDH-PSI from Arabidopsis. Determined by electron microscopy at 3.25 Å resolution. Released 16 Mar 2022.
- Method
- Electron microscopy
- Resolution
- 3.25 Å
- Organism
- Arabidopsis thaliana
- Chains
- 16
- Atoms
- 35,603
- Mol. weight
- 597.8 kDa
- Ligands
- CLA, PQN, LHG, BCR
- Released
- 16 Mar 2022
Explore 7WFD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7WFD contains 166 α-helices and 67 β-strands across 16 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A1: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-55 | 3 | |
| α-helix | 77-106 | 30 | |
| α-helix | 114-120 | 7 | |
| β-strand | 127-128 | 2 | 25 |
| β-strand | 131-132 | 2 | 25 |
| α-helix | 133 | 1 | |
| α-helix | 139-157 | 19 | |
| α-helix | 170-172 | 3 | |
| α-helix | 174-176 | 3 | |
| α-helix | 181-211 | 31 | |
| α-helix | 217-226 | 10 | |
| α-helix | 234-237 | 4 | |
Chain A3: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-64 | 3 | |
| β-strand | 88 | 1 | 26 |
| β-strand | 91 | 1 | 26 |
| α-helix | 95-114 | 20 | |
| α-helix | 116-119 | 4 | |
| β-strand | 140 | 1 | 27 |
| β-strand | 144 | 1 | 27 |
| α-helix | 152-175 | 24 | |
| α-helix | 188-190 | 3 | |
| α-helix | 215-246 | 32 | |
| α-helix | 250-258 | 9 | |
Chain A4: 12 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-64 | 3 | |
| α-helix | 82-84 | 3 | |
| α-helix | 86-108 | 23 | |
| α-helix | 112-118 | 7 | |
| α-helix | 141-162 | 22 | |
| α-helix | 164-166 | 3 | |
| α-helix | 181-182 | 2 | |
| α-helix | 188-190 | 3 | |
| α-helix | 199-224 | 26 | |
| α-helix | 230-239 | 10 | |
| α-helix | 241-243 | 3 | |
| α-helix | 246-249 | 4 | |
Chain A6: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 73-75 | 3 | |
| α-helix | 97-130 | 34 | |
| α-helix | 138-140 | 3 | |
| α-helix | 148-150 | 3 | |
| α-helix | 152-173 | 22 | |
| β-strand | 184 | 1 | 28 |
| β-strand | 187 | 1 | 28 |
| α-helix | 189-191 | 3 | |
| β-strand | 193 | 1 | 29 |
| β-strand | 196 | 1 | 29 |
| α-helix | 199-202 | 4 | |
| α-helix | 215-239 | 25 | |
| α-helix | 247-256 | 10 | |
Chain AA: 43 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 14-16 | 3 | 1 |
| α-helix | 24-27 | 4 | |
| β-strand | 42 | 1 | 2 |
| α-helix | 44-51 | 8 | |
| α-helix | 56-59 | 4 | |
| α-helix | 63-94 | 32 | |
| α-helix | 98-103 | 6 | |
| β-strand | 111-113 | 3 | 3 |
| α-helix | 121-124 | 4 | |
| β-strand | 126-127 | 2 | 4 |
| β-strand | 133-134 | 2 | 4 |
| β-strand | 135-136 | 2 | 3 |
| α-helix | 141-147 | 7 | |
| α-helix | 153-175 | 23 | |
| α-helix | 176-180 | 5 | |
| β-strand | 181-183 | 3 | 1 |
| α-helix | 185-188 | 4 | |
| α-helix | 192-196 | 5 | |
| α-helix | 197-204 | 8 | |
| α-helix | 205-213 | 9 | |
| α-helix | 214-218 | 5 | |
| α-helix | 219-227 | 9 | |
| α-helix | 237-242 | 6 | |
| α-helix | 244-250 | 7 | |
| α-helix | 253-256 | 4 | |
| α-helix | 259-262 | 4 | |
| α-helix | 266-269 | 4 | |
| β-strand | 279 | 1 | 5 |
| β-strand | 286 | 1 | 5 |
| α-helix | 288-305 | 18 | |
| β-strand | 309 | 1 | 6 |
| β-strand | 317 | 1 | 6 |
| α-helix | 319-323 | 5 | |
| α-helix | 338-342 | 5 | |
| α-helix | 346-370 | 25 | |
| α-helix | 381-411 | 31 | |
| α-helix | 422-429 | 8 | |
| α-helix | 431-445 | 15 | |
| α-helix | 446-451 | 6 | |
| α-helix | 452-461 | 10 | |
| α-helix | 465-467 | 3 | |
| β-strand | 469 | 1 | 7 |
| β-strand | 474 | 1 | 7 |
| α-helix | 479-494 | 16 | |
| α-helix | 522-525 | 4 | |
| α-helix | 528-553 | 26 | |
| α-helix | 564-567 | 4 | |
| α-helix | 586-615 | 30 | |
| β-strand | 618-620 | 3 | 8 |
| β-strand | 626-628 | 3 | 8 |
| α-helix | 634-637 | 4 | |
| α-helix | 641-643 | 3 | |
| α-helix | 644-650 | 7 | |
| α-helix | 651-652 | 2 | |
| α-helix | 665-686 | 22 | |
| α-helix | 689-704 | 16 | |
| β-strand | 713 | 1 | 2 |
| α-helix | 716-718 | 3 | |
| α-helix | 719-749 | 31 | |
Chain AB: 42 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17 | 1 | 9 |
| α-helix | 19-26 | 8 | |
| α-helix | 27-29 | 3 | |
| α-helix | 31-33 | 3 | |
| α-helix | 39-71 | 33 | |
| α-helix | 74-77 | 4 | |
| α-helix | 81-83 | 3 | |
| β-strand | 89-90 | 2 | 10 |
| α-helix | 98-103 | 6 | |
| β-strand | 113-114 | 2 | 10 |
| α-helix | 120-126 | 7 | |
| α-helix | 132-155 | 24 | |
| α-helix | 165-168 | 4 | |
| α-helix | 173-177 | 5 | |
| α-helix | 178-185 | 8 | |
| α-helix | 186-193 | 8 | |
| α-helix | 194-198 | 5 | |
| α-helix | 199-202 | 4 | |
| α-helix | 223-227 | 5 | |
| α-helix | 230-234 | 5 | |
| α-helix | 242-243 | 2 | |
| β-strand | 261 | 1 | 11 |
| β-strand | 268 | 1 | 11 |
| α-helix | 270-288 | 19 | |
| β-strand | 291 | 1 | 12 |
| β-strand | 299 | 1 | 12 |
| α-helix | 301-305 | 5 | |
| α-helix | 324-327 | 4 | |
| α-helix | 330-352 | 23 | |
| α-helix | 365-392 | 28 | |
| α-helix | 393-397 | 5 | |
| α-helix | 409-413 | 5 | |
| α-helix | 415-445 | 31 | |
| α-helix | 449-451 | 3 | |
| β-strand | 454-455 | 2 | 13 |
| α-helix | 458-465 | 8 | |
| α-helix | 485-488 | 4 | |
| α-helix | 494-501 | 8 | |
| α-helix | 514-539 | 26 | |
| α-helix | 550-553 | 4 | |
| α-helix | 572-603 | 32 | |
| α-helix | 606-612 | 7 | |
| α-helix | 616-619 | 4 | |
| α-helix | 620-625 | 6 | |
| α-helix | 626-627 | 2 | |
| α-helix | 629-632 | 4 | |
| β-strand | 635-636 | 2 | 14 |
| β-strand | 639-640 | 2 | 14 |
| α-helix | 644-665 | 22 | |
| α-helix | 672-684 | 13 | |
| β-strand | 696 | 1 | 9 |
| α-helix | 698-701 | 4 | |
| α-helix | 702-731 | 30 | |
Chain AC: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 15 |
| α-helix | 16-20 | 5 | |
| β-strand | 27-30 | 4 | 16 |
| β-strand | 38-41 | 4 | 16 |
| α-helix | 45-47 | 3 | |
| β-strand | 65-68 | 4 | 15 |
Chain AD: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 76 | 1 | 17 |
| β-strand | 93-100 | 8 | 18 |
| β-strand | 104-106 | 3 | 17 |
| β-strand | 114-116 | 3 | 17 |
| α-helix | 117 | 1 | |
| β-strand | 119-125 | 7 | 18 |
| α-helix | 128-137 | 10 | |
| α-helix | 138-142 | 5 | |
| β-strand | 146-152 | 7 | 18 |
| β-strand | 155-159 | 5 | 18 |
| β-strand | 180-181 | 2 | 15 |
| α-helix | 185-187 | 3 | |
| α-helix | 189-190 | 2 | |
8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Photosystem I P700 chlorophyll a apoprotein A1 | AA | protein | 750 | Arabidopsis thaliana | P56766 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A2 | AB | protein | 734 | Arabidopsis thaliana | P56767 (AlphaFold model) |
| Photosystem I iron-sulfur center | AC | protein | 81 | Arabidopsis thaliana | P62090 (AlphaFold model) |
| Photosystem I reaction center subunit II-2, chloroplastic | AD | protein | 204 | Arabidopsis thaliana | Q9SA56 (AlphaFold model) |
| Photosystem I reaction center subunit IV A, chloroplastic | AE | protein | 143 | Arabidopsis thaliana | Q9S831 |
| Photosystem I reaction center subunit III, chloroplastic | AF | protein | 221 | Arabidopsis thaliana | Q9SHE8 |
| Photosystem I reaction center subunit V, chloroplastic | AG | protein | 160 | Arabidopsis thaliana | Q9S7N7 |
| Photosystem I reaction center subunit VI-2, chloroplastic | AH | protein | 145 | Arabidopsis thaliana | Q9SUI6 |
| Photosystem I reaction center subunit VIII | AI | protein | 37 | Arabidopsis thaliana | P56768 |
| Photosystem I reaction center subunit IX | AJ | protein | 44 | Arabidopsis thaliana | P56769 |
| Photosystem I reaction center subunit psaK, chloroplastic | AK | protein | 130 | Arabidopsis thaliana | Q9SUI5 |
| Photosystem I reaction center subunit XI, chloroplastic | AL | protein | 219 | Arabidopsis thaliana | Q9SUI4 |
4 more molecules are not listed.
Sequence of entity 1 (AA), FASTA
>7WFD_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains AA)
MIIRSPEPEVKILVDRDPIKTSFEEWAKPGHFSRTIAKGPDTTTWIWNLHADAHDFDSHT
SDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLSDPTHIGPSAQVVWPIVG
QEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAALMLFAGWFHYHK
AAPKLAWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPKEIPLPHEF
ILNRDLLAQLYPSFAEGATPFFTLNWSKYSEFLTFRGGLDPVTGGLWLTDIAHHHLAIAI
LFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSLNLAMLGSL
TIIVAHHMYSMPPYPYLATDYATQLSLFTHHMWIGGFLIVGAAAHAAIFMVRDYDPTNRY
NDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVF
AQWIQNTHALAPGVTAPGETASTSLTWGGGELVAVGGKVALLPIPLGTADFLVHHIHAFT
IHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNA
ISVVIFHFSWKMQSDVWGSISDQGVVTHITGGNFAQSSITINGWLRDFLWAQASQVIQSY
GSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSII
QGRAVGVTHYLLGGIATTWAFFLARIIAVG
Sequence of entity 2 (AB), FASTA
>7WFD_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains AB)
MALRFPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEERLYQNIFASHFGQLAIIFLW
TSGNLFHVAWQGNFETWVQDPLHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGV
YQWWYTIGLRTNEDLYTGALFLLFLSALSLIGGWLHLQPKWKPRVSWFKNAESRLNHHLS
GLFGVSSLAWTGHLVHVAIPASRGEYVRWNNFLNVLPHPQGLGPLFTGQWNLYAQNPDSS
SHLFGTSQGSGTAILTLLGGFHPQTQSLWLTDMAHHHLAIAILFLIAGHMYRTNFGIGHS
IKDLLEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAF
IAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNPEQNEDNVLARMLDHKEAIIS
HLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSS
TSGPAFNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALD
ARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHIT
LWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMFLFGHLVWATG
FMFLISWRGYWQELIETLAWAHERTPLANLIRWKDKPVALSIVQARLVGLAHFSVGYIFT
YAAFLIASTSGKFG
Sequence of entity 3 (AC), FASTA
>7WFD_3 Photosystem I iron-sulfur center (chains AC)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY
Sequence of entity 4 (AD), FASTA
>7WFD_4 Photosystem I reaction center subunit II-2, chloroplastic (chains AD)
MATQAAGIFSPAITTTTSAVKKLHLFSSSHRPKSLSFTKTAIRAEKTESSSAAPAVKEAP
VGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAIMREGP
NLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPGREGVGL
NMRSIGKNVSPIEVKFTGKQSYDL
Sequence of entity 5 (AE), FASTA
>7WFD_5 Photosystem I reaction center subunit IV A, chloroplastic (chains AE)
MAMTTASTVFVLPANVTSVAGASSSRSSVSFLPMRNAGSRLVVRAAEDPAPASSSSKDSP
AAAAAPDGATATKPKPPPIGPKRGSKVKILRRESYWFKNVGSVVAVDQDPKTRYPVVVRF
AKVNYANISTNNYALDEVEEVAA
Sequence of entity 6 (AF), FASTA
>7WFD_6 Photosystem I reaction center subunit III, chloroplastic (chains AF)
MSLTIPANLVLNPRSNKSLTQSVPKSSARFVCSDDKSSSSTPQSMKAFSAAVALSSILLS
APMPAVADISGLTPCKDSKQFAKREKQQIKKLESSLKLYAPESAPALALNAQIEKTKRRF
DNYGKYGLLCGSDGLPHLIVNGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAISGEKK
PAMKEIIIDVPLASRIIFRGFIWPVAAYREFLNGDLIAKDV
Sequence of entity 7 (AG), FASTA
>7WFD_7 Photosystem I reaction center subunit V, chloroplastic (chains AG)
MATSASALLSPTTFSTAISHKNPNSISFHGLRPLRLGGSSSALPKLSTTGRKSSSAVVRA
ELSPSIVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGKTHFEAGDDRAKEYVSLLK
SNDPIGFNIVDVLAWGSIGHIVAYYILATSSNGYDPSFFG
Sequence of entity 8 (AH), FASTA
>7WFD_8 Photosystem I reaction center subunit VI-2, chloroplastic (chains AH)
MASFATIAAVQPSAAVKGLGGSSLAGAKLFIKPSRQSFKTKSTRAGAVVAKYGDKSVYFD
LEDLGNTTGQWDVYGSDAPSPYNPLQSKFFETFAAPFTKRGLLLKFLILGGGSLLTYVSA
NSTGDVLPIKRGPQEPPKLGPRGKL
Sequence of entity 9 (AI), FASTA
>7WFD_9 Photosystem I reaction center subunit VIII (chains AI)
MTTFNNLPSIFVPLVGLVFPAIAMASLFLHIQKNKIF
Sequence of entity 10 (AJ), FASTA
>7WFD_10 Photosystem I reaction center subunit IX (chains AJ)
MRDLKTYLSVAPVLSTLWFGSLAGLLIEINRLFPDALTFPFFSF
Sequence of entity 11 (AK), FASTA
>7WFD_11 Photosystem I reaction center subunit psaK, chloroplastic (chains AK)
MASTMMTTLPQFNGLRATKISAAPVQGLASVQPMRRKGNGALGAKCDFIGSSTNLIMVTS
TTLMLFAGRFGLAPSANRKATAGLRLEARDSGLQTGDPAGFTLADTLACGTVGHIIGVGV
VLGLKNIGAI
Sequence of entity 12 (AL), FASTA
>7WFD_12 Photosystem I reaction center subunit XI, chloroplastic (chains AL)
MAASASPMASQLRSSFSSASLSQRLAVPKGISGAPFGVSPTKRVSSFTVRAVKSDKTTFQ
VVQPINGDPFIGSLETPVTSSPLIAWYLSNLPGYRTAVNPLLRGVEVGLAHGFFLVGPFV
KAGPLRNTAYAGSAGSLAAAGLVVILSMCLTIYGISSFKEGEPSIAPSLTLTGRKKQPDQ
LQTADGWAKFTGGFFFGGISGVTWAYFLLYVLDLPYFVK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 143 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 8 |
| BCR | Beta-carotene | C40 H56 | 26 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| LMU | Dodecyl-alpha-D-maltoside | C24 H46 O11 | 5 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 1 |
| LUT | (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | C40 H56 O2 | 5 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 3 |
| CHL | Chlorophyll B | C55 H70 Mg N4 O6 | 11 |
| XAT | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-… | C40 H56 O4 | 4 |
Primary citation
Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana. Su, X., Cao, D., Pan, X. et al. Mol Plant (2022) 15:454-467. DOI 10.1016/j.molp.2022.01.020 · PubMed
Other PDB entries of the same protein (UniProt P56766 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9WLS 2.18 Å, PSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method
- 8J6Z 2.79 Å, Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
- 8J7A 3.06 Å, Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 1 (PSI-ST1)
- 8J7B 3.22 Å, Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 2 (PSI-ST2)
- 7WFE 3.25 Å, Right PSI in the cyclic electron transfer supercomplex NDH-PSI from Arabidopsis
- 7WG5 3.89 Å, Cyclic electron transport supercomplex NDH-PSI from Arabidopsis
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