4Y28: Plant photosystem I super-complex
The structure of plant photosystem I super-complex at 2.8 angstrom resolution. Determined by X-ray diffraction at 2.8 Å resolution. Released 19 Aug 2015.
- Method
- X-ray diffraction
- Resolution
- 2.8 Å
- Organism
- Pisum sativum
- Chains
- 16
- Atoms
- 35,653
- Mol. weight
- 554.63 kDa
- Ligands
- CL0, CLA, SF4, PQN
- Released
- 19 Aug 2015
Explore 4Y28 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4Y28 contains 166 α-helices and 61 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: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-48 | 3 | |
| α-helix | 70-99 | 30 | |
| α-helix | 105-113 | 9 | |
| β-strand | 120 | 1 | 26 |
| β-strand | 125 | 1 | 26 |
| α-helix | 131-149 | 19 | |
| α-helix | 154-158 | 5 | |
| α-helix | 170-172 | 3 | |
| α-helix | 174-202 | 29 | |
| α-helix | 210-219 | 10 | |
| α-helix | 226-230 | 5 | |
Chain 2: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 96-124 | 29 | |
| α-helix | 125-129 | 5 | |
| α-helix | 150-164 | 15 | |
| α-helix | 167-172 | 6 | |
| α-helix | 198-201 | 4 | |
| α-helix | 213-242 | 30 | |
| α-helix | 246-255 | 10 | |
| α-helix | 262-264 | 3 | |
Chain 3: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 95-125 | 31 | |
| α-helix | 136-140 | 5 | |
| α-helix | 154-177 | 24 | |
| α-helix | 218-220 | 3 | |
| α-helix | 221-243 | 23 | |
| α-helix | 244-248 | 5 | |
| α-helix | 252-261 | 10 | |
| α-helix | 268-271 | 4 | |
Chain 4: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 85-118 | 34 | |
| α-helix | 126-128 | 3 | |
| α-helix | 138-161 | 24 | |
| β-strand | 169 | 1 | 25 |
| β-strand | 175 | 1 | 25 |
| α-helix | 187-189 | 3 | |
| α-helix | 200-225 | 26 | |
| α-helix | 229-238 | 10 | |
| α-helix | 240-242 | 3 | |
| α-helix | 245-248 | 4 | |
Chain A: 48 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-24 | 2 | 1 |
| β-strand | 50 | 1 | 2 |
| α-helix | 52-59 | 8 | |
| α-helix | 64-67 | 4 | |
| α-helix | 71-99 | 29 | |
| α-helix | 106-109 | 4 | |
| α-helix | 117-118 | 2 | |
| β-strand | 119 | 1 | 3 |
| α-helix | 129-132 | 4 | |
| β-strand | 134-135 | 2 | 4 |
| β-strand | 141-142 | 2 | 4 |
| α-helix | 143 | 1 | |
| β-strand | 144 | 1 | 3 |
| α-helix | 145 | 1 | |
| α-helix | 149-155 | 7 | |
| α-helix | 161-183 | 23 | |
| α-helix | 184-188 | 5 | |
| β-strand | 190-191 | 2 | 1 |
| α-helix | 192 | 1 | |
| α-helix | 193-197 | 5 | |
| α-helix | 199-205 | 7 | |
| α-helix | 206-212 | 7 | |
| α-helix | 213-221 | 9 | |
| α-helix | 222-226 | 5 | |
| α-helix | 227-235 | 9 | |
| α-helix | 243-244 | 2 | |
| α-helix | 246-250 | 5 | |
| α-helix | 254-257 | 4 | |
| α-helix | 260-263 | 4 | |
| α-helix | 277-279 | 3 | |
| α-helix | 296-313 | 18 | |
| β-strand | 317 | 1 | 5 |
| β-strand | 325 | 1 | 5 |
| α-helix | 327-332 | 6 | |
| α-helix | 346-350 | 5 | |
| α-helix | 354-378 | 25 | |
| α-helix | 389-420 | 32 | |
| α-helix | 432-435 | 4 | |
| α-helix | 436-438 | 3 | |
| α-helix | 439-469 | 31 | |
| α-helix | 473-475 | 3 | |
| α-helix | 487-497 | 11 | |
| β-strand | 500 | 1 | 6 |
| β-strand | 504 | 1 | 6 |
| α-helix | 513-515 | 3 | |
| β-strand | 521-523 | 3 | 7 |
| β-strand | 526-529 | 4 | 7 |
| α-helix | 531-533 | 3 | |
| α-helix | 536-561 | 26 | |
| α-helix | 572-575 | 4 | |
| α-helix | 594-619 | 26 | |
| α-helix | 620-624 | 5 | |
| β-strand | 626-628 | 3 | 7 |
| β-strand | 634-636 | 3 | 7 |
| α-helix | 642-645 | 4 | |
| α-helix | 649-651 | 3 | |
| α-helix | 652-658 | 7 | |
| α-helix | 659-660 | 2 | |
| α-helix | 662-665 | 4 | |
| α-helix | 673-693 | 21 | |
| α-helix | 697-713 | 17 | |
| β-strand | 721 | 1 | 2 |
| α-helix | 724-726 | 3 | |
| α-helix | 727-757 | 31 | |
Chain B: 44 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-13 | 4 | |
| β-strand | 17 | 1 | 8 |
| α-helix | 19-26 | 8 | |
| α-helix | 31-33 | 3 | |
| α-helix | 39-71 | 33 | |
| α-helix | 75-79 | 5 | |
| α-helix | 85-86 | 2 | |
| β-strand | 87-90 | 4 | 9 |
| α-helix | 98-104 | 7 | |
| β-strand | 113-115 | 3 | 9 |
| α-helix | 116 | 1 | |
| α-helix | 120-127 | 8 | |
| α-helix | 132-155 | 24 | |
| α-helix | 162-164 | 3 | |
| α-helix | 165-168 | 4 | |
| α-helix | 171-177 | 7 | |
| α-helix | 178-185 | 8 | |
| α-helix | 186-193 | 8 | |
| α-helix | 194-198 | 5 | |
| α-helix | 199-201 | 3 | |
| α-helix | 209-211 | 3 | |
| α-helix | 223-227 | 5 | |
| α-helix | 230-234 | 5 | |
| α-helix | 237-239 | 3 | |
| β-strand | 261-262 | 2 | 10 |
| β-strand | 267-268 | 2 | 10 |
| α-helix | 270-287 | 18 | |
| β-strand | 291 | 1 | 11 |
| β-strand | 299 | 1 | 11 |
| α-helix | 301-307 | 7 | |
| α-helix | 322-327 | 6 | |
| α-helix | 330-352 | 23 | |
| α-helix | 365-396 | 32 | |
| α-helix | 401-403 | 3 | |
| α-helix | 407-413 | 7 | |
| α-helix | 415-445 | 31 | |
| α-helix | 449-451 | 3 | |
| β-strand | 455 | 1 | 12 |
| α-helix | 458-467 | 10 | |
| α-helix | 484-488 | 5 | |
| α-helix | 494-501 | 8 | |
| α-helix | 514-539 | 26 | |
| α-helix | 563-565 | 3 | |
| α-helix | 572-602 | 31 | |
| α-helix | 606-612 | 7 | |
| α-helix | 616-618 | 3 | |
| α-helix | 619-625 | 7 | |
| α-helix | 626-627 | 2 | |
| β-strand | 635 | 1 | 13 |
| β-strand | 640 | 1 | 13 |
| α-helix | 644-665 | 22 | |
| α-helix | 668-683 | 16 | |
| β-strand | 696 | 1 | 8 |
| α-helix | 699-701 | 3 | |
| α-helix | 702-732 | 31 | |
Chain C: 2 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 | 55-57 | 3 | |
| β-strand | 65-68 | 4 | 19 |
Chain D: 5 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-74 | 3 | |
| β-strand | 83 | 1 | 21 |
| β-strand | 91 | 1 | 17 |
| α-helix | 93-97 | 5 | |
| β-strand | 101-107 | 7 | 22 |
| β-strand | 112-114 | 3 | 21 |
| β-strand | 120-122 | 3 | 21 |
| β-strand | 126-132 | 7 | 22 |
| α-helix | 136-146 | 11 | |
| β-strand | 153-157 | 5 | 22 |
| β-strand | 165-168 | 4 | 22 |
| β-strand | 187-188 | 2 | 19 |
| α-helix | 195-197 | 3 | |
| α-helix | 198-201 | 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 |
|---|
| Photosystem I P700 chlorophyll a apoprotein A1 | A | protein | 758 | Pisum sativum | P05310 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A2 | B | protein | 733 | Pisum sativum | P05311 (AlphaFold model) |
| Photosystem I reaction center subunit VIII | I | protein | 30 | Pisum sativum | P17227 (AlphaFold model) |
| Photosystem I reaction center subunit IX | J | protein | 42 | Pisum sativum | D5MAL3 (AlphaFold model) |
| Photosystem I reaction center subunit III | F | protein | 154 | Pisum sativum | A0A0M3KL12 |
| photosystem I reaction center | G | protein | 97 | Pisum sativum | A0A0M3KL13 |
| Putative uncharacterized protein | L | protein | 167 | Pisum sativum | E1C9L1 |
| Photosystem I iron-sulfur center | C | protein | 81 | Pisum sativum | P10793 |
| Photosystem I reaction center subunit II, chloroplastic | D | protein | 147 | Pisum sativum | E1C9K8 |
| Photosystem I reaction center subunit IV A, chloroplastic | E | protein | 66 | Pisum sativum | E1C9K6 |
| Photosystem I reaction center subunit VI | H | protein | 90 | Pisum sativum | A0A0M3KL10 |
| Photosystem I reaction center subunit X psaK | K | protein | 129 | Pisum sativum | A0A0M3KL11 |
4 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>4Y28_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
MIIRSPEPKVQILADPEVKIILDRDPIKTSFEQWAKPGHFSRTIAKGPDTTTWIWNLHAD
AHDFDSHTSDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLNDPTHIRPSA
QVVWPIVGQEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAGLMLF
AGWFHYHKAAPKLAWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPK
EIPLPHEFILNRDLLAQLYPSFAEGATPFFTLNWSKYADFLTFRGGLDPLTGGLWLTDIA
HHHLAIAILFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSI
NLAMLGSLTIVVAQHMYSMPPYPYLATDYATQLSLFTHHMWIGGFLIVGAAAHAAIFMVR
DYDPTTRYNDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDT
AIQLQPVFAQWIQNTHALAPGTTAPGATASTSLTWGGGDLVAVGNKVALLPIPLGTADFL
VHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFL
GLFWMYNSISVVIFHFSWKMQSDVWGTINDQGVVTHITTGNFAQSSITINGWLRDFLWAQ
ASQVIQSYGSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAT
QPRALSIVQGRAVGVTHYLLGGIATTWAFFLARIIAVG
Sequence of entity 2 (B), FASTA
>4Y28_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
MALRLPRFSQGIAQDPTTRRIWFGIATAHDFESHDDITEGRLYQNIFASHFGQLAIIFLW
TSGNLFHVAWQGNFEAWVQDPFHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGV
YQWWYTIGLRTNEDLYTGAIFLLFLSFISLLAGWLHLQPKWKPSVSWFKNAESRLNHHLS
GLFGVSSLAWAGHLVHVAIPGSRGEYVRWNNFLDVLPYPQGLGPLLTGQWNLYAQNPSSS
NHLFGTTQGAGTAILTILGGFHPQTQSLWLTDMAHHHLAIAFLFLIGGLMYRTNFGIGHS
IKYILEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAF
IAQDFTTQAALYTHHQYIAGFIMTGAFAHGPIFFIRDYNPEQNADNVLARMLEHKEAIIS
HLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSS
TNGPALNAGRNIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALD
ARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDDFYLAVFWMLNTIGWVTFYWHWKHIT
LWRGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYTPLVCNSLSVWAWMFLFGHLVWATG
FMFLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVALSIVQARLVGLVHFSVGYIFT
YAAFLIASTSGKF
Sequence of entity 3 (I), FASTA
>4Y28_3 Photosystem I reaction center subunit VIII (chains I)
NLPSLFVPLVGLLFPAVAMASLFLHVEKRL
Sequence of entity 4 (J), FASTA
>4Y28_4 Photosystem I reaction center subunit IX (chains J)
MRDLKTYLSVAPVASTLWFAALAGLLIEINRLFPDALTFPFF
Sequence of entity 5 (F), FASTA
>4Y28_5 Photosystem I reaction center subunit III (chains F)
DISGLTPCKESKQFAKREKQSIKKLESSLKIYAADSAPALAINATIEKTKRRFDNYAKQG
LLCGADGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDEKKPTQKEII
IDVPLASRLVFRGFSWPIAAYRELLNGELVAKDV
Sequence of entity 6 (G), FASTA
>4Y28_6 photosystem I reaction center (chains G)
AELNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDSRAKEYAGVS
KSAAALVDVLAWGSIGHIVAYYILATSSNGYDPKFFG
Sequence of entity 7 (L), FASTA
>4Y28_7 Putative uncharacterized protein (chains L)
AVQSEKPTYQVVQPINGDPFIGSLETPVTSSPLVAWYLSNLPGYRTAVNPLLRGIEVGLA
HGFFLVGPFVKAGPLRNTEIAGQAGSLAAAGLVVILSICLTIYGISSFNEGDPSTAPSLT
LTGRKKQPDQLQTADGWAKFTGGFFFGGISGVIWAFFLLYVLDLPYY
Sequence of entity 8 (C), FASTA
>4Y28_8 Photosystem I iron-sulfur center (chains C)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY
Sequence of entity 9 (D), FASTA
>4Y28_9 Photosystem I reaction center subunit II, chloroplastic (chains D)
KEAPVGTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR
EGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQG
VGVNFRSIGKNVSPIEVKFTGKQPYDL
Sequence of entity 10 (E), FASTA
>4Y28_10 Photosystem I reaction center subunit IV A, chloroplastic (chains E)
PPIGPKRGAKVKILRQESYWYKGTGSVVTVDQDPNTRYPVVVRFNKVNYANVSTNNYALD
EVEEVK
Sequence of entity 11 (H), FASTA
>4Y28_11 Photosystem I reaction center subunit VI (chains H)
SVYFDLEDIGNTTGQWDLYGSDAPSPYSPLQSKFFETFAAPFTKRGLLLKFLILGGGSTL
AYFSTTASGDILPIVKGPQLPPKLGPRGKL
Sequence of entity 12 (K), FASTA
>4Y28_12 Photosystem I reaction center subunit X psaK (chains K)
MATSMMTTLPQFTGLRPQLKPSPIQGLVAAQPMTRRKGKGALGVRCDFIGSSTNVIMVAS
TTLMLFAGRFGLAPSANRKATAGLKLEVRDSGLQTGDPAGFTLADTLACGTVGHIIGVGV
VLGLKTLCM
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CL0 | Chlorophyll a isomer | C55 H72 Mg N4 O5 | 1 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 146 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 5 |
| BCR | Beta-carotene | C40 H56 | 21 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 7 |
| CA | Calcium ion | Ca | 1 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 1 |
| LMU | Dodecyl-alpha-D-maltoside | C24 H46 O11 | 2 |
| LUT | (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | C40 H56 O2 | 10 |
| CHL | Chlorophyll B | C55 H70 Mg N4 O6 | 9 |
| ZEX | (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylc… | C40 H56 O2 | 1 |
Primary citation
The structure of plant photosystem I super-complex at 2.8 angstrom resolution. Mazor, Y., Borovikova, A., Nelson, N. Elife (2015) 4:e07433-e07433. DOI 10.7554/eLife.07433 · PubMed
Other PDB entries of the same protein (UniProt P05310 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7DKZ 2.39 Å, Structure of plant photosystem I-light harvesting complex I supercomplex
- 5L8R 2.6 Å, The structure of plant photosystem I super-complex at 2.6 angstrom resolution.
- 4XK8 2.8 Å, Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution
- 4RKU 3.0 Å, Crystal structure of plant Photosystem I at 3 Angstrom resolution
- 2WSC 3.3 Å, Improved Model of Plant Photosystem I
- 3LW5 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
- 2WSE 3.49 Å, Improved Model of Plant Photosystem I
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