8J7A: Chlorophyll a-b binding protein 6, chloroplastic
Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 1 (PSI-ST1). Determined by electron microscopy at 3.06 Å resolution. Released 15 Nov 2023.
- Method
- Electron microscopy
- Resolution
- 3.06 Å
- Organism
- Arabidopsis thaliana
- Chains
- 16
- Atoms
- 34,246
- Mol. weight
- 587.02 kDa
- Ligands
- CLA, XAT, BCR, DGD
- Released
- 15 Nov 2023
Explore 8J7A in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8J7A contains 171 α-helices and 72 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 1: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-55 | 3 | |
| α-helix | 77-107 | 31 | |
| α-helix | 142-157 | 16 | |
| α-helix | 162-166 | 5 | |
| α-helix | 181-211 | 31 | |
| α-helix | 217-226 | 10 | |
| α-helix | 234-237 | 4 | |
Chain 2: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 60-62 | 3 | |
| α-helix | 84-117 | 34 | |
| α-helix | 128-130 | 3 | |
| α-helix | 137-160 | 24 | |
| β-strand | 167 | 1 | 1 |
| β-strand | 175 | 1 | 1 |
| α-helix | 186-189 | 4 | |
| α-helix | 199-230 | 32 | |
| α-helix | 234-243 | 10 | |
Chain 3: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 60-65 | 6 | |
| β-strand | 88 | 1 | 2 |
| β-strand | 91 | 1 | 2 |
| α-helix | 93-123 | 31 | |
| α-helix | 128-130 | 3 | |
| α-helix | 141-143 | 3 | |
| α-helix | 152-175 | 24 | |
| α-helix | 179-181 | 3 | |
| α-helix | 203-206 | 4 | |
| α-helix | 215-245 | 31 | |
| α-helix | 250-259 | 10 | |
Chain 4: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-64 | 3 | |
| α-helix | 86-119 | 34 | |
| α-helix | 128-131 | 4 | |
| α-helix | 139-162 | 24 | |
| β-strand | 169 | 1 | 3 |
| β-strand | 177 | 1 | 3 |
| α-helix | 178-180 | 3 | |
| α-helix | 188-190 | 3 | |
| α-helix | 199-225 | 27 | |
| α-helix | 230-239 | 10 | |
Chain A: 45 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 42 | 1 | 4 |
| 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 | 5 |
| α-helix | 121-124 | 4 | |
| β-strand | 126-127 | 2 | 6 |
| β-strand | 133-134 | 2 | 6 |
| β-strand | 135-136 | 2 | 5 |
| α-helix | 137 | 1 | |
| α-helix | 141-147 | 7 | |
| α-helix | 153-179 | 27 | |
| α-helix | 182-184 | 3 | |
| α-helix | 185-188 | 4 | |
| α-helix | 191-196 | 6 | |
| α-helix | 197-204 | 8 | |
| α-helix | 205-213 | 9 | |
| α-helix | 214-218 | 5 | |
| α-helix | 219-226 | 8 | |
| α-helix | 231-233 | 3 | |
| α-helix | 235-236 | 2 | |
| α-helix | 237-242 | 6 | |
| α-helix | 244-250 | 7 | |
| α-helix | 252-256 | 5 | |
| α-helix | 259-262 | 4 | |
| α-helix | 266-271 | 6 | |
| β-strand | 279 | 1 | 7 |
| β-strand | 286 | 1 | 7 |
| α-helix | 288-305 | 18 | |
| β-strand | 309 | 1 | 8 |
| β-strand | 317 | 1 | 8 |
| α-helix | 319-325 | 7 | |
| α-helix | 338-343 | 6 | |
| α-helix | 346-369 | 24 | |
| α-helix | 381-412 | 32 | |
| α-helix | 422-428 | 7 | |
| α-helix | 431-461 | 31 | |
| α-helix | 465-467 | 3 | |
| α-helix | 479-490 | 12 | |
| β-strand | 492 | 1 | 9 |
| β-strand | 496 | 1 | 9 |
| β-strand | 513-515 | 3 | 10 |
| β-strand | 518-521 | 4 | 10 |
| α-helix | 523-525 | 3 | |
| α-helix | 528-553 | 26 | |
| α-helix | 564-567 | 4 | |
| β-strand | 573 | 1 | 11 |
| α-helix | 577-579 | 3 | |
| β-strand | 582 | 1 | 11 |
| α-helix | 586-615 | 30 | |
| β-strand | 618-620 | 3 | 10 |
| β-strand | 626-628 | 3 | 10 |
| α-helix | 634-637 | 4 | |
| α-helix | 641-643 | 3 | |
| α-helix | 644-650 | 7 | |
| α-helix | 651-652 | 2 | |
| α-helix | 656-658 | 3 | |
| α-helix | 665-686 | 22 | |
| α-helix | 690-704 | 15 | |
| β-strand | 713 | 1 | 4 |
| α-helix | 716-718 | 3 | |
| α-helix | 719-748 | 30 | |
Chain B: 44 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-13 | 4 | |
| β-strand | 17 | 1 | 12 |
| α-helix | 19-26 | 8 | |
| α-helix | 31-33 | 3 | |
| α-helix | 39-71 | 33 | |
| α-helix | 74-79 | 6 | |
| α-helix | 81-83 | 3 | |
| β-strand | 87-90 | 4 | 13 |
| α-helix | 98-103 | 6 | |
| β-strand | 113-115 | 3 | 13 |
| α-helix | 120-126 | 7 | |
| α-helix | 132-156 | 25 | |
| α-helix | 159-161 | 3 | |
| α-helix | 162-164 | 3 | |
| α-helix | 165-168 | 4 | |
| α-helix | 171-176 | 6 | |
| α-helix | 177-185 | 9 | |
| 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 | |
| α-helix | 270-287 | 18 | |
| β-strand | 291 | 1 | 14 |
| β-strand | 299 | 1 | 14 |
| α-helix | 301-306 | 6 | |
| β-strand | 318 | 1 | 15 |
| α-helix | 322-328 | 7 | |
| α-helix | 330-352 | 23 | |
| α-helix | 365-396 | 32 | |
| β-strand | 406 | 1 | 15 |
| α-helix | 407-413 | 7 | |
| α-helix | 415-445 | 31 | |
| α-helix | 449-451 | 3 | |
| β-strand | 455 | 1 | 16 |
| α-helix | 458-466 | 9 | |
| α-helix | 477-479 | 3 | |
| α-helix | 484-489 | 6 | |
| α-helix | 494-501 | 8 | |
| α-helix | 514-539 | 26 | |
| α-helix | 550-553 | 4 | |
| β-strand | 559 | 1 | 17 |
| β-strand | 568 | 1 | 17 |
| α-helix | 573-603 | 31 | |
| α-helix | 607-612 | 6 | |
| α-helix | 616-619 | 4 | |
| α-helix | 620-625 | 6 | |
| α-helix | 626-627 | 2 | |
| α-helix | 629-632 | 4 | |
| β-strand | 635 | 1 | 18 |
| β-strand | 640 | 1 | 18 |
| α-helix | 644-665 | 22 | |
| α-helix | 668-683 | 16 | |
| β-strand | 696 | 1 | 12 |
| α-helix | 699-701 | 3 | |
| α-helix | 702-733 | 32 | |
Chain C: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 19 |
| α-helix | 16-20 | 5 | |
| β-strand | 27-30 | 4 | 20 |
| β-strand | 38-41 | 4 | 20 |
| α-helix | 45-47 | 3 | |
| α-helix | 55-57 | 3 | |
| β-strand | 65-68 | 4 | 19 |
| α-helix | 74-77 | 4 | |
Chain D: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-68 | 5 | |
| α-helix | 72-75 | 4 | |
| β-strand | 76 | 1 | 21 |
| β-strand | 84 | 1 | 22 |
| α-helix | 86-90 | 5 | |
| β-strand | 93-100 | 8 | 23 |
| β-strand | 104-107 | 4 | 21 |
| β-strand | 113-116 | 4 | 21 |
| α-helix | 117 | 1 | |
| β-strand | 119-125 | 7 | 23 |
| α-helix | 128-137 | 10 | |
| α-helix | 138-142 | 5 | |
| β-strand | 146-151 | 6 | 23 |
| β-strand | 157-161 | 5 | 23 |
| β-strand | 180-181 | 2 | 19 |
| α-helix | 185-187 | 3 | |
| α-helix | 188-190 | 3 | |
| α-helix | 191-194 | 4 | |
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 |
|---|
| Chlorophyll a-b binding protein 6, chloroplastic | 1 | protein | 241 | Arabidopsis thaliana | Q01667 (AlphaFold model) |
| Photosystem I chlorophyll a/b-binding protein 2, chloroplastic | 2 | protein | 257 | Arabidopsis thaliana | Q9SYW8 (AlphaFold model) |
| Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic | 3 | protein | 273 | Arabidopsis thaliana | Q9SY97 (AlphaFold model) |
| Chlorophyll a-b binding protein 4, chloroplastic | 4 | protein | 251 | Arabidopsis thaliana | P27521 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A1 | A | protein | 750 | Arabidopsis thaliana | P56766 |
| Photosystem I P700 chlorophyll a apoprotein A2 | B | protein | 734 | Arabidopsis thaliana | P56767 |
| Photosystem I iron-sulfur center | C | protein | 81 | Arabidopsis thaliana | P62090 |
| Photosystem I reaction center subunit II-2, chloroplastic | D | protein | 204 | Arabidopsis thaliana | Q9SA56 |
| Photosystem I reaction center subunit IV A, chloroplastic | E | protein | 143 | Arabidopsis thaliana | Q9S831 |
| Photosystem I reaction center subunit III, chloroplastic | F | protein | 221 | Arabidopsis thaliana | Q9SHE8 |
| Photosystem I reaction center subunit V, chloroplastic | G | protein | 160 | Arabidopsis thaliana | Q9S7N7 |
| Photosystem I reaction center subunit VI-2, chloroplastic | H | protein | 145 | Arabidopsis thaliana | Q9SUI6 |
4 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>8J7A_1 Chlorophyll a-b binding protein 6, chloroplastic (chains 1)
MASNSLMSCGIAAVYPSLLSSSKSKFVSAGVPLPNAGNVGRIRMAAHWMPGEPRPAYLDG
SAPGDFGFDPLGLGEVPANLERYKESELIHCRWAMLAVPGILVPEALGYGNWVKAQEWAA
LPGGQATYLGNPVPWGTLPTILAIEFLAIAFVEHQRSMEKDPEKKKYPGGAFDPLGYSKD
PKKLEELKVKEIKNGRLALLAFVGFCVQQSAYPGTGPLENLATHLADPWHNNIGDIVIPF
N
Sequence of entity 2 (2), FASTA
>8J7A_2 Photosystem I chlorophyll a/b-binding protein 2, chloroplastic (chains 2)
MASSLCASSAIAAISSPSFLGGKKLRLKKKLTVPAVSRPDASVRAVAADPDRPIWFPGST
PPEWLDGSLPGDFGFDPLGLSSDPDSLKWNVQAEIVHCRWAMLGAAGIFIPEFLTKIGIL
NTPSWYTAGEQEYFTDKTTLFVVELILIGWAEGRRWADIIKPGSVNTDPVFPNNKLTGTD
VGYPGGLWFDPLGWGSGSPAKLKELRTKEIKNGRLAMLAVMGAWFQHIYTGTGPIDNLFA
HLADPGHATIFAAFTPK
Sequence of entity 3 (3), FASTA
>8J7A_3 Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic (chains 3)
MAAQALVSSSLTSSVQTARQIFGSKPVASASQKKSSFVVKAAATPPVKQGANRPLWFASS
QSLSYLDGSLPGDYGFDPLGLSDPEGTGGFIEPRWLAYGEIINGRFAMLGAAGAIAPEIL
GKAGLIPAETALPWFQTGVIPPAGTYTYWADNYTLFVLEMALMGFAEHRRLQDWYNPGSM
GKQYFLGLEKGLAGSGNPAYPGGPFFNPLGFGKDEKSLKELKLKEVKNGRLAMLAILGYF
IQGLVTGVGPYQNLLDHLADPVNNNVLTSLKFH
Sequence of entity 4 (4), FASTA
>8J7A_4 Chlorophyll a-b binding protein 4, chloroplastic (chains 4)
MATVTTHASASIFRPCTSKPRFLTGSSGRLNRDLSFTSIGSSAKTSSFKVEAKKGEWLPG
LASPDYLTGSLAGDNGFDPLGLAEDPENLKWFVQAELVNGRWAMLGVAGMLLPEVFTKIG
IINVPEWYDAGKEQYFASSSTLFVIEFILFHYVEIRRWQDIKNPGSVNQDPIFKQYSLPK
GEVGYPGGIFNPLNFAPTQEAKEKELANGRLAMLAFLGFVVQHNVTGKGPFENLLQHLSD
PWHNTIVQTFN
Sequence of entity 5 (A), FASTA
>8J7A_5 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
MIIRSPEPEVKILVDRDPIKTSFEEWAKPGHFSRTIAKGPDTTTWIWNLHADAHDFDSHT
SDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLSDPTHIGPSAQVVWPIVG
QEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAALMLFAGWFHYHK
AAPKLAWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPKEIPLPHEF
ILNRDLLAQLYPSFAEGATPFFTLNWSKYSEFLTFRGGLDPVTGGLWLTDIAHHHLAIAI
LFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSLNLAMLGSL
TIIVAHHMYSMPPYPYLATDYATQLSLFTHHMWIGGFLIVGAAAHAAIFMVRDYDPTNRY
NDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVF
AQWIQNTHALAPGVTAPGETASTSLTWGGGELVAVGGKVALLPIPLGTADFLVHHIHAFT
IHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNA
ISVVIFHFSWKMQSDVWGSISDQGVVTHITGGNFAQSSITINGWLRDFLWAQASQVIQSY
GSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSII
QGRAVGVTHYLLGGIATTWAFFLARIIAVG
Sequence of entity 6 (B), FASTA
>8J7A_6 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
MALRFPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEERLYQNIFASHFGQLAIIFLW
TSGNLFHVAWQGNFETWVQDPLHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGV
YQWWYTIGLRTNEDLYTGALFLLFLSALSLIGGWLHLQPKWKPRVSWFKNAESRLNHHLS
GLFGVSSLAWTGHLVHVAIPASRGEYVRWNNFLNVLPHPQGLGPLFTGQWNLYAQNPDSS
SHLFGTSQGSGTAILTLLGGFHPQTQSLWLTDMAHHHLAIAILFLIAGHMYRTNFGIGHS
IKDLLEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAF
IAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNPEQNEDNVLARMLDHKEAIIS
HLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSS
TSGPAFNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALD
ARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHIT
LWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMFLFGHLVWATG
FMFLISWRGYWQELIETLAWAHERTPLANLIRWKDKPVALSIVQARLVGLAHFSVGYIFT
YAAFLIASTSGKFG
Sequence of entity 7 (C), FASTA
>8J7A_7 Photosystem I iron-sulfur center (chains C)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY
Sequence of entity 8 (D), FASTA
>8J7A_8 Photosystem I reaction center subunit II-2, chloroplastic (chains D)
MATQAAGIFSPAITTTTSAVKKLHLFSSSHRPKSLSFTKTAIRAEKTESSSAAPAVKEAP
VGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAIMREGP
NLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPGREGVGL
NMRSIGKNVSPIEVKFTGKQSYDL
Sequence of entity 9 (E), FASTA
>8J7A_9 Photosystem I reaction center subunit IV A, chloroplastic (chains E)
MAMTTASTVFVLPANVTSVAGASSSRSSVSFLPMRNAGSRLVVRAAEDPAPASSSSKDSP
AAAAAPDGATATKPKPPPIGPKRGSKVKILRRESYWFKNVGSVVAVDQDPKTRYPVVVRF
AKVNYANISTNNYALDEVEEVAA
Sequence of entity 10 (F), FASTA
>8J7A_10 Photosystem I reaction center subunit III, chloroplastic (chains F)
MSLTIPANLVLNPRSNKSLTQSVPKSSARFVCSDDKSSSSTPQSMKAFSAAVALSSILLS
APMPAVADISGLTPCKDSKQFAKREKQQIKKLESSLKLYAPESAPALALNAQIEKTKRRF
DNYGKYGLLCGSDGLPHLIVNGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAISGEKK
PAMKEIIIDVPLASRIIFRGFIWPVAAYREFLNGDLIAKDV
Sequence of entity 11 (G), FASTA
>8J7A_11 Photosystem I reaction center subunit V, chloroplastic (chains G)
MATSASALLSPTTFSTAISHKNPNSISFHGLRPLRLGGSSSALPKLSTTGRKSSSAVVRA
ELSPSIVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGKTHFEAGDDRAKEYVSLLK
SNDPIGFNIVDVLAWGSIGHIVAYYILATSSNGYDPSFFG
Sequence of entity 12 (H), FASTA
>8J7A_12 Photosystem I reaction center subunit VI-2, chloroplastic (chains H)
MASFATIAAVQPSAAVKGLGGSSLAGAKLFIKPSRQSFKTKSTRAGAVVAKYGDKSVYFD
LEDLGNTTGQWDVYGSDAPSPYNPLQSKFFETFAAPFTKRGLLLKFLILGGGSLLTYVSA
NSTGDVLPIKRGPQEPPKLGPRGKL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 138 |
| XAT | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-… | C40 H56 O4 | 3 |
| BCR | Beta-carotene | C40 H56 | 25 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 1 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| CL0 | Chlorophyll a isomer | C55 H72 Mg N4 O5 | 1 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 2 |
| LUT | (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | C40 H56 O2 | 5 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 6 |
| CHL | Chlorophyll B | C55 H70 Mg N4 O6 | 12 |
Primary citation
Regulatory dynamics of the higher-plant PSI-LHCI supercomplex during state transitions. Wu, J., Chen, S., Wang, C. et al. Mol Plant (2023) 16:1937-1950. DOI 10.1016/j.molp.2023.11.002 · PubMed
Other PDB entries of the same protein (UniProt Q01667 (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
- 6ZOO 2.74 Å, Photosystem I reduced Plastocyanin Complex
- 8J6Z 2.79 Å, Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
- 4XK8 2.8 Å, Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution
- 9GBI 3.13 Å, Cryo-EM structure of Arabidopsis thaliana PSI-LHCI wild-type
- 8J7B 3.22 Å, Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 2 (PSI-ST2)
- 7WFD 3.25 Å, Left PSI in the cyclic electron transport supercomplex NDH-PSI from Arabidopsis
- 7WFE 3.25 Å, Right PSI in the cyclic electron transfer supercomplex NDH-PSI from Arabidopsis
- 9GC2 3.29 Å, Cryo-EM structure of Arabidopsis thaliana PSI-LHCI- a603-NH mutant
- 2WSC 3.3 Å, Improved Model of Plant Photosystem I
- 2O01 3.4 Å, The Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution
- 2WSF 3.48 Å, Improved Model of Plant Photosystem I
Browse structure collections
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