9GC2: Arabidopsis thaliana PSI-LHCI- a603-NH mutant
Cryo-EM structure of Arabidopsis thaliana PSI-LHCI- a603-NH mutant. Determined by electron microscopy at 3.29 Å resolution. Released 13 Aug 2025.
- Method
- Electron microscopy
- Resolution
- 3.29 Å
- Organism
- Arabidopsis thaliana
- Chains
- 17
- Atoms
- 35,543
- Mol. weight
- 547.88 kDa
- Ligands
- DGD, SF4, PQN, LMG
- Released
- 13 Aug 2025
Explore 9GC2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9GC2 contains 162 α-helices and 66 β-strands across 17 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: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-55 | 3 | |
| α-helix | 77-102 | 26 | |
| α-helix | 114-119 | 6 | |
| β-strand | 127-128 | 2 | 1 |
| β-strand | 131-132 | 2 | 1 |
| α-helix | 138-157 | 20 | |
| α-helix | 162-166 | 5 | |
| α-helix | 170-172 | 3 | |
| α-helix | 184-211 | 28 | |
| α-helix | 217-226 | 10 | |
| α-helix | 234-237 | 4 | |
Chain 2: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 60-62 | 3 | |
| α-helix | 84-116 | 33 | |
| α-helix | 122-124 | 3 | |
| α-helix | 137-160 | 24 | |
| β-strand | 167 | 1 | 2 |
| β-strand | 175 | 1 | 2 |
| β-strand | 180 | 1 | 3 |
| β-strand | 183 | 1 | 3 |
| α-helix | 186-189 | 4 | |
| α-helix | 199-230 | 32 | |
| α-helix | 234-243 | 10 | |
Chain 3: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 58 | 1 | 4 |
| α-helix | 62-65 | 4 | |
| β-strand | 76 | 1 | 4 |
| β-strand | 88 | 1 | 5 |
| β-strand | 91 | 1 | 5 |
| α-helix | 93-122 | 30 | |
| α-helix | 152-175 | 24 | |
| α-helix | 179-181 | 3 | |
| α-helix | 188-192 | 5 | |
| α-helix | 203-206 | 4 | |
| α-helix | 215-245 | 31 | |
| α-helix | 250-259 | 10 | |
| α-helix | 266-270 | 5 | |
Chain 4: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-64 | 3 | |
| α-helix | 86-119 | 34 | |
| α-helix | 139-162 | 24 | |
| α-helix | 178-180 | 3 | |
| α-helix | 188-190 | 3 | |
| α-helix | 199-225 | 27 | |
| α-helix | 230-239 | 10 | |
Chain A: 44 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 14-16 | 3 | 6 |
| α-helix | 24-27 | 4 | |
| α-helix | 34-37 | 4 | |
| β-strand | 42 | 1 | 7 |
| 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 | 8 |
| α-helix | 121-124 | 4 | |
| β-strand | 135-136 | 2 | 8 |
| α-helix | 137 | 1 | |
| α-helix | 141-148 | 8 | |
| α-helix | 154-179 | 26 | |
| β-strand | 181-183 | 3 | 6 |
| α-helix | 184 | 1 | |
| α-helix | 185-188 | 4 | |
| α-helix | 191-196 | 6 | |
| α-helix | 197-205 | 9 | |
| α-helix | 206-213 | 8 | |
| 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 | 259-263 | 5 | |
| α-helix | 266-271 | 6 | |
| β-strand | 280 | 1 | 9 |
| β-strand | 285 | 1 | 9 |
| α-helix | 288-305 | 18 | |
| α-helix | 319-325 | 7 | |
| α-helix | 338-344 | 7 | |
| α-helix | 346-370 | 25 | |
| α-helix | 381-412 | 32 | |
| α-helix | 422-428 | 7 | |
| α-helix | 431-461 | 31 | |
| α-helix | 465-467 | 3 | |
| α-helix | 479-494 | 16 | |
| β-strand | 513-515 | 3 | 10 |
| β-strand | 518-521 | 4 | 10 |
| α-helix | 528-553 | 26 | |
| α-helix | 564-567 | 4 | |
| β-strand | 573 | 1 | 11 |
| 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 | 641-644 | 4 | |
| α-helix | 645-650 | 6 | |
| α-helix | 654-657 | 4 | |
| α-helix | 665-686 | 22 | |
| α-helix | 689-704 | 16 | |
| β-strand | 713 | 1 | 7 |
| α-helix | 716-718 | 3 | |
| α-helix | 719-749 | 31 | |
Chain B: 40 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-14 | 5 | |
| β-strand | 17 | 1 | 12 |
| α-helix | 19-26 | 8 | |
| α-helix | 39-71 | 33 | |
| α-helix | 74-79 | 6 | |
| α-helix | 81-83 | 3 | |
| β-strand | 87-90 | 4 | 13 |
| α-helix | 98-104 | 7 | |
| β-strand | 113-115 | 3 | 13 |
| α-helix | 120-126 | 7 | |
| α-helix | 132-156 | 25 | |
| α-helix | 162-164 | 3 | |
| α-helix | 165-168 | 4 | |
| α-helix | 171-177 | 7 | |
| α-helix | 178-184 | 7 | |
| α-helix | 185-193 | 9 | |
| α-helix | 194-198 | 5 | |
| α-helix | 199-202 | 4 | |
| α-helix | 223-227 | 5 | |
| α-helix | 230-234 | 5 | |
| α-helix | 237-239 | 3 | |
| α-helix | 270-287 | 18 | |
| β-strand | 291 | 1 | 14 |
| β-strand | 299 | 1 | 14 |
| α-helix | 301-306 | 6 | |
| α-helix | 322-328 | 7 | |
| α-helix | 330-351 | 22 | |
| α-helix | 365-396 | 32 | |
| α-helix | 407-413 | 7 | |
| α-helix | 415-445 | 31 | |
| α-helix | 449-451 | 3 | |
| β-strand | 455 | 1 | 15 |
| α-helix | 458-467 | 10 | |
| α-helix | 477-479 | 3 | |
| α-helix | 484-490 | 7 | |
| α-helix | 494-501 | 8 | |
| α-helix | 514-539 | 26 | |
| α-helix | 550-553 | 4 | |
| β-strand | 559 | 1 | 16 |
| β-strand | 568 | 1 | 16 |
| α-helix | 572-603 | 32 | |
| α-helix | 607-612 | 6 | |
| α-helix | 616-619 | 4 | |
| α-helix | 620-625 | 6 | |
| α-helix | 626-627 | 2 | |
| β-strand | 635 | 1 | 17 |
| β-strand | 640 | 1 | 17 |
| α-helix | 644-665 | 22 | |
| α-helix | 668-683 | 16 | |
| β-strand | 696 | 1 | 12 |
| α-helix | 702-732 | 31 | |
Chain C: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 18 |
| α-helix | 16-20 | 5 | |
| β-strand | 27-30 | 4 | 19 |
| β-strand | 38-41 | 4 | 19 |
| α-helix | 45-47 | 3 | |
| α-helix | 53-56 | 4 | |
| β-strand | 65-68 | 4 | 18 |
| α-helix | 74-77 | 4 | |
Chain D: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 76 | 1 | 20 |
| β-strand | 84 | 1 | 21 |
| α-helix | 86-90 | 5 | |
| β-strand | 93-100 | 8 | 22 |
| β-strand | 104-107 | 4 | 20 |
| β-strand | 113-116 | 4 | 20 |
| α-helix | 117 | 1 | |
| β-strand | 119-125 | 7 | 22 |
| α-helix | 128-137 | 10 | |
| α-helix | 138-142 | 5 | |
| β-strand | 146-151 | 6 | 22 |
| β-strand | 157-159 | 3 | 22 |
| β-strand | 180-181 | 2 | 18 |
| α-helix | 188-190 | 3 | |
| α-helix | 201-203 | 3 | |
9 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 | 206 | Arabidopsis thaliana | Q01667 (AlphaFold model) |
| Photosystem I chlorophyll a/b-binding protein 2, chloroplastic | 2 | protein | 214 | Arabidopsis thaliana | Q9SYW8 (AlphaFold model) |
| Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic | 3 | protein | 234 | Arabidopsis thaliana | Q9SY97 (AlphaFold model) |
| Chlorophyll a-b binding protein 4, chloroplastic | 4 | protein | 199 | Arabidopsis thaliana | P27521 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A1 | A | protein | 750 | Arabidopsis thaliana | A0A8F5S1X0 |
| Photosystem I P700 chlorophyll a apoprotein A2 | B | protein | 734 | Arabidopsis thaliana | A0A8F5P166 |
| Photosystem I iron-sulfur center | C | protein | 81 | Arabidopsis thaliana | P62090 |
| Photosystem I reaction center subunit II-2, chloroplastic | D | protein | 160 | Arabidopsis thaliana | Q9SA56 |
| Photosystem I reaction center subunit IV B, chloroplastic | E | protein | 99 | Arabidopsis thaliana | Q9S714 |
| Photosystem I reaction center subunit III, chloroplastic | F | protein | 154 | Arabidopsis thaliana | Q9SHE8 |
| Photosystem I reaction center subunit V, chloroplastic | G | protein | 100 | Arabidopsis thaliana | Q9S7N7 |
| Photosystem I reaction center subunit VI-1, chloroplastic | H | protein | 95 | Arabidopsis thaliana | Q9SUI7 |
5 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>9GC2_1 Chlorophyll a-b binding protein 6, chloroplastic (chains 1)
AGNVGRIRMAAHWMPGEPRPAYLDGSAPGDFGFDPLGLGEVPANLERYKESELIHCRWAM
LAVPGILVPEALGYGNWVKAQEWAALPGGQATYLGNPVPWGTLPTILAIEFLAIAFVEHQ
RSMEKDPEKKKYPGGAFDPLGYSKDPKKLEELKVKEIKNGRLALLAFVGFCVQQSAYPGT
GPLENLATHLADPWHNNIGDIVIPFN
Sequence of entity 2 (2), FASTA
>9GC2_2 Photosystem I chlorophyll a/b-binding protein 2, chloroplastic (chains 2)
RAVAADPDRPIWFPGSTPPEWLDGSLPGDFGFDPLGLSSDPDSLKWNVQAEIVHCRWAML
GAAGIFIPEFLTKIGILNTPSWYTAGEQEYFTDKTTLFVVELILIGWAEGRRWADIIKPG
SVNTDPVFPNNKLTGTDVGYPGGLWFDPLGWGSGSPAKLKELRTKEIKNGRLAMLAVMGA
WFQHIYTGTGPIDNLFAHLADPGHATIFAAFTPK
Sequence of entity 3 (3), FASTA
>9GC2_3 Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic (chains 3)
KAAATPPVKQGANRPLWFASSQSLSYLDGSLPGDYGFDPLGLSDPEGTGGFIEPRWLAYG
EIIHGRFAMLGAAGAIAPEILGKAGLIPAETALPWFQTGVIPPAGTYTYWADNYTLFVLE
MALMGFAEHRRLQDWYNPGSMGKQYFLGLEKGLAGSGNPAYPGGPFFNPLGFGKDEKSLK
ELKLKEVKNGRLAMLAILGYFIQGLVTGVGPYQNLLDHLADPVNNNVLTSLKFH
Sequence of entity 4 (4), FASTA
>9GC2_4 Chlorophyll a-b binding protein 4, chloroplastic (chains 4)
KKGEWLPGLASPDYLTGSLAGDNGFDPLGLAEDPENLKWFVQAELVHGRWAMLGVAGMLL
PEVFTKIGIINVPEWYDAGKEQYFASSSTLFVIEFILFHYVEIRRWQDIKNPGSVNQDPI
FKQYSLPKGEVGYPGGIFNPLNFAPTQEAKEKELANGRLAMLAFLGFVVQHNVTGKGPFE
NLLQHLSDPWHNTIVQTFN
Sequence of entity 5 (A), FASTA
>9GC2_5 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
MIIRSPEPEVKILVDRDPIKTSFEEWAKPGHFSRTIAKGPDTTTWIWNLHADAHDFDSHT
SDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLSDPTHIGPSAQVVWSIVG
QEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGGLVFAALMLFAGWFHYHK
AAPKLAWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPKEIPLPHEF
ILNRDLLAQLYPSFAEGATPFFTLNWSKYAEFLTFRGGLDPVTGGLWLTDIAHHHLAIAI
LFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSINLAMLGSL
TIVVAHHMYSMPPYPYLATDYGTQLSLFTHHMWIGGFLIVGAAAHAAIFMVRDYDPTTRY
NDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVF
AQWIQNTHALAPGTTAPGATTSTSLTWGGGDLVAVGGKVALLPIPLGTADFLVHHIHAFT
IHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNA
ISVVIFHFSWKMQSDVWGSISDQGVVTHITGGNFAQSSITINGWLRDFLWAQASQVIQSY
GSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSIV
QGRAVGVTHYLLGGIATTWAFFLARIIAVG
Sequence of entity 6 (B), FASTA
>9GC2_6 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
MALRFPRFSQGLAQDPTTRRIWFGIATAHDFENHDDITEERLYQNIFASHFGQLAIIFLW
TSGNLFHVAWQGNFEAWVQDPLHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGV
YQWWYTIGLRTNGDLYTGALFLLFLSAISLIAGWLHLQPKWKPSVSWFKNAESRLNHHLS
GLFGVSSLAWTGHLVHVAIPGSRGEYVRWNNFLGVLPHPQGLGPLFTGQWNLYAQNPDSS
SHLFGTSQGTGTAILTLLGGFHPQTQSLWLTDIAHHHLAIAILFLVAGHMYRTNFGIGHS
IKDLLEAHIPPGGRLGRGHRGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAF
IAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNPEQNEDNVLARMLDHKEAIIS
HLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSS
TNSPAFNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALD
ARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHIT
LWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMFLFGHLVWATG
FMFLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVALSIVQARLVGLAHFSVGYIFT
YAAFLIASTSGKFG
Sequence of entity 7 (C), FASTA
>9GC2_7 Photosystem I iron-sulfur center (chains C)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY
Sequence of entity 8 (D), FASTA
>9GC2_8 Photosystem I reaction center subunit II-2, chloroplastic (chains D)
EKTESSSAAPAVKEAPVGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQ
IFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKD
GVYPEKANPGREGVGLNMRSIGKNVSPIEVKFTGKQSYDL
Sequence of entity 9 (E), FASTA
>9GC2_9 Photosystem I reaction center subunit IV B, chloroplastic (chains E)
AAEDTPPATASSDSSSTTAAAAPAKVPAAKAKPPPIGPKRGSKVKILRKESYWYKNVGSV
VAVDQDPKTRYPVVVRFAKVNYANISTNNYALDEVEEVK
Sequence of entity 10 (F), FASTA
>9GC2_10 Photosystem I reaction center subunit III, chloroplastic (chains F)
DISGLTPCKDSKQFAKREKQQIKKLESSLKLYAPESAPALALNAQIEKTKRRFDNYGKYG
LLCGSDGLPHLIVNGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAISGEKKPAMKEII
IDVPLASRIIFRGFIWPVAAYREFLNGDLIAKDV
Sequence of entity 11 (G), FASTA
>9GC2_11 Photosystem I reaction center subunit V, chloroplastic (chains G)
ELSPSIVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGKTHFEAGDDRAKEYVSLLK
SNDPIGFNIVDVLAWGSIGHIVAYYILATSSNGYDPSFFG
Sequence of entity 12 (H), FASTA
>9GC2_12 Photosystem I reaction center subunit VI-1, chloroplastic (chains H)
KYGDKSVYFDLEDLGNTTGQWDVYGSDAPSPYNPLQSKFFETFAAPFTKRGLLLKFLILG
GGSLLTYVSATSTGEVLPIKRGPQEPPKLGPRGKL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 1 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 3 |
| BCR | Beta-carotene | C40 H56 | 27 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 2 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 5 |
| XAT | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-… | C40 H56 O4 | 4 |
| LUT | (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | C40 H56 O2 | 5 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 142 |
| CHL | Chlorophyll B | C55 H70 Mg N4 O6 | 12 |
Primary citation
Structural determinants for red-shifted absorption in higher-plants Photosystem I. Capaldi, S., Guardini, Z., Montepietra, D. et al. New Phytol (2025) 248:2331-2346. DOI 10.1111/nph.70562 · 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
- 8J7A 3.06 Å, Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 1 (PSI-ST1)
- 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
- 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
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