4RKU: Plant Photosystem I
Crystal structure of plant Photosystem I at 3 Angstrom resolution. Determined by X-ray diffraction at 3.0 Å resolution. Released 4 Feb 2015.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organism
- Pisum sativum
- Chains
- 17
- Atoms
- 34,540
- Mol. weight
- 528.53 kDa
- Ligands
- PQN, BCR, LHG, CLA
- Released
- 4 Feb 2015
Explore 4RKU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4RKU contains 154 α-helices and 60 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: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 70-100 | 31 | |
| α-helix | 104-108 | 5 | |
| α-helix | 110-113 | 4 | |
| α-helix | 131-144 | 14 | |
| α-helix | 157-159 | 3 | |
| α-helix | 163-165 | 3 | |
| α-helix | 175-202 | 28 | |
| α-helix | 208-217 | 10 | |
Chain 2: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 100-121 | 22 | |
| α-helix | 157-177 | 21 | |
| α-helix | 219-240 | 22 | |
| α-helix | 255-258 | 4 | |
Chain 3: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 104-125 | 22 | |
| α-helix | 157-163 | 7 | |
| α-helix | 166-171 | 6 | |
| α-helix | 173-179 | 7 | |
| α-helix | 225-228 | 4 | |
| α-helix | 230-248 | 19 | |
| α-helix | 253-262 | 10 | |
Chain 4: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 86-100 | 15 | |
| α-helix | 104-116 | 13 | |
| α-helix | 124-126 | 3 | |
| α-helix | 139-163 | 24 | |
| α-helix | 202-224 | 23 | |
| α-helix | 231-239 | 9 | |
| α-helix | 247-249 | 3 | |
Chain A: 44 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-45 | 4 | |
| β-strand | 50 | 1 | 1 |
| α-helix | 52-59 | 8 | |
| α-helix | 64-66 | 3 | |
| α-helix | 71-102 | 32 | |
| α-helix | 106-111 | 6 | |
| β-strand | 119 | 1 | 2 |
| α-helix | 129-132 | 4 | |
| β-strand | 134-135 | 2 | 3 |
| β-strand | 141-142 | 2 | 3 |
| β-strand | 144 | 1 | 2 |
| α-helix | 149-155 | 7 | |
| α-helix | 161-187 | 27 | |
| α-helix | 190-192 | 3 | |
| α-helix | 193-197 | 5 | |
| α-helix | 199-205 | 7 | |
| α-helix | 206-210 | 5 | |
| α-helix | 212-221 | 10 | |
| α-helix | 222-226 | 5 | |
| α-helix | 227-233 | 7 | |
| α-helix | 239-241 | 3 | |
| α-helix | 243-244 | 2 | |
| α-helix | 245-250 | 6 | |
| α-helix | 252-256 | 5 | |
| α-helix | 260-263 | 4 | |
| α-helix | 276-279 | 4 | |
| α-helix | 296-312 | 17 | |
| β-strand | 317 | 1 | 4 |
| β-strand | 325 | 1 | 4 |
| α-helix | 327-333 | 7 | |
| β-strand | 336 | 1 | 5 |
| β-strand | 340 | 1 | 5 |
| α-helix | 346-349 | 4 | |
| α-helix | 354-376 | 23 | |
| α-helix | 389-420 | 32 | |
| α-helix | 432-435 | 4 | |
| α-helix | 439-469 | 31 | |
| β-strand | 477 | 1 | 6 |
| β-strand | 482 | 1 | 6 |
| α-helix | 487-497 | 11 | |
| β-strand | 500 | 1 | 7 |
| β-strand | 504 | 1 | 7 |
| α-helix | 513-515 | 3 | |
| β-strand | 521 | 1 | 8 |
| β-strand | 526 | 1 | 9 |
| β-strand | 529 | 1 | 8 |
| α-helix | 531-533 | 3 | |
| α-helix | 536-561 | 26 | |
| α-helix | 572-574 | 3 | |
| β-strand | 581 | 1 | 10 |
| β-strand | 590 | 1 | 10 |
| α-helix | 594-609 | 16 | |
| α-helix | 612-623 | 12 | |
| β-strand | 626-628 | 3 | 9 |
| β-strand | 634-636 | 3 | 9 |
| α-helix | 642-645 | 4 | |
| α-helix | 649-652 | 4 | |
| α-helix | 653-658 | 6 | |
| α-helix | 664-666 | 3 | |
| α-helix | 673-687 | 15 | |
| α-helix | 690-693 | 4 | |
| α-helix | 697-713 | 17 | |
| β-strand | 721 | 1 | 1 |
| α-helix | 724-726 | 3 | |
| α-helix | 727-757 | 31 | |
Chain B: 42 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-13 | 4 | |
| β-strand | 17 | 1 | 11 |
| α-helix | 19-26 | 8 | |
| α-helix | 31-33 | 3 | |
| α-helix | 39-70 | 32 | |
| α-helix | 75-78 | 4 | |
| β-strand | 87-90 | 4 | 12 |
| α-helix | 98-103 | 6 | |
| β-strand | 113-115 | 3 | 12 |
| α-helix | 120-127 | 8 | |
| α-helix | 132-155 | 24 | |
| α-helix | 162-164 | 3 | |
| α-helix | 165-168 | 4 | |
| α-helix | 172-177 | 6 | |
| α-helix | 178-185 | 8 | |
| α-helix | 186-193 | 8 | |
| α-helix | 194-198 | 5 | |
| α-helix | 199-203 | 5 | |
| α-helix | 223-227 | 5 | |
| α-helix | 231-234 | 4 | |
| α-helix | 237-239 | 3 | |
| β-strand | 261-262 | 2 | 13 |
| β-strand | 267-268 | 2 | 13 |
| α-helix | 270-287 | 18 | |
| β-strand | 291 | 1 | 14 |
| β-strand | 299 | 1 | 14 |
| α-helix | 301-307 | 7 | |
| α-helix | 322-327 | 6 | |
| α-helix | 330-354 | 25 | |
| α-helix | 365-386 | 22 | |
| α-helix | 389-392 | 4 | |
| α-helix | 393-397 | 5 | |
| α-helix | 415-445 | 31 | |
| α-helix | 449-451 | 3 | |
| β-strand | 455 | 1 | 15 |
| α-helix | 458-465 | 8 | |
| α-helix | 487-489 | 3 | |
| α-helix | 493-501 | 9 | |
| α-helix | 514-539 | 26 | |
| α-helix | 550-552 | 3 | |
| α-helix | 563-565 | 3 | |
| α-helix | 572-602 | 31 | |
| α-helix | 606-612 | 7 | |
| α-helix | 616-619 | 4 | |
| α-helix | 620-625 | 6 | |
| α-helix | 629-632 | 4 | |
| β-strand | 635 | 1 | 16 |
| β-strand | 640 | 1 | 16 |
| α-helix | 644-665 | 22 | |
| α-helix | 668-683 | 16 | |
| β-strand | 696 | 1 | 11 |
| α-helix | 699-701 | 3 | |
| α-helix | 702-732 | 31 | |
Chain C: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 17 |
| α-helix | 16-20 | 5 | |
| β-strand | 27-30 | 4 | 18 |
| β-strand | 38-41 | 4 | 18 |
| α-helix | 45-47 | 3 | |
| α-helix | 55-57 | 3 | |
| β-strand | 65-68 | 4 | 17 |
| α-helix | 74-77 | 4 | |
Chain D: 3 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 80-82 | 3 | |
| β-strand | 83 | 1 | 19 |
| β-strand | 87 | 1 | 20 |
| β-strand | 91 | 1 | 21 |
| α-helix | 94-97 | 4 | |
| β-strand | 101-105 | 5 | 22 |
| β-strand | 107 | 1 | 23 |
| β-strand | 112-113 | 2 | 19 |
| β-strand | 121-122 | 2 | 19 |
| β-strand | 126 | 1 | 23 |
| β-strand | 129-132 | 4 | 22 |
| α-helix | 136-146 | 11 | |
| β-strand | 153-157 | 5 | 22 |
| β-strand | 165-167 | 3 | 22 |
| β-strand | 187-188 | 2 | 17 |
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 |
|---|
| Photosystem I P700 chlorophyll a apoprotein A1 | A | protein | 721 | Pisum sativum | P05310 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A2 | B | protein | 731 | Pisum sativum | P05311 (AlphaFold model) |
| Photosystem I iron-sulfur center | C | protein | 80 | Pisum sativum | P10793 (AlphaFold model) |
| Photosystem I reaction center subunit II, chloroplastic | D | protein | 137 | Pisum sativum | E1C9K8 (AlphaFold model) |
| Photosystem I reaction center subunit IV B, chloroplastic | E | protein | 63 | Pisum sativum | E1C9K6 |
| Photosystem I reaction center subunit III, chloroplastic | F | protein | 152 | Pisum sativum | A0A0H2UKZ4 |
| Photosystem I reaction center subunit V, chloroplastic | G | protein | 84 | Pisum sativum | P20120 |
| Photosystem I reaction center subunit VI, chloroplastic | H | protein | 82 | Pisum sativum | E1C9K9 |
| Photosystem I reaction center subunit VIII | I | protein | 26 | Pisum sativum | P17227 |
| Photosystem I reaction center subunit IX | J | protein | 40 | Pisum sativum | D5MAL3 |
| Photosystem I reaction center subunit X psaK | K | protein | 72 | Pisum sativum | E1C9L3 |
| Photosystem I reaction center subunit XI, chloroplastic | L | protein | 163 | Pisum sativum | E1C9L1 |
5 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>4RKU_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
GHFSRTIAKGPDTTTWIWNLHADAHDFDSHTSDLEEISRKVFSAHFGQLSIIFLWLSGMY
FHGARFSNYEAWLNDPTHIRPSAQVVWPIVGQEILNGDVGGGFRGIQITSGFFQIWRASG
ITSELQLYCTAIGALVFAGLMLFAGWFHYHKAAPKLAWFQDVESMLNHHLAGLLGLGSLS
WARHQVHVSLPINQFLNAGVDPKEIPLPHEFILNRDLLAQLYPSFAEGATPFFTLNWSKY
ADFLTFRGGLDPLTGGLWLTDIAHHHLAIAILFLIAGHMYRTNWGIGHGIKDILEAHKGP
FTGQGHKGLYEILTTSWHAQLSINLAMLGSLTIVVAQHMYSMPPYPYLATDYATQLSLFT
HHMWIGGFLIVGAAAHAAIFMVRDYDPTTRYNDLLDRVLRHRDAIISHLNWVCIFLGFHS
FGLYIHNDTMSALGRPQDMFSDTAIQLQPVFAQWIQNTHALAPGTTAPGATASTSLTWGG
GDLVAVGNKVALLPIPLGTADFLVHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLGF
RFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSISVVIFHFSWKMQSDVWGSINDQGVVTHI
TGGNFAQSSITINGWLRDFLWAQASQVIQSYGSSLSAYGLFFLGAHFVWAFSLMFLFSGR
GYWQELIESIVWAHNKLKVAPATQPRALSIVQGRAVGVTHYLLGGIATTWAFFLARIIAV
G
Sequence of entity 2 (B), FASTA
>4RKU_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
LRIPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEGRLYQNIFASHFGQLAIIFLWTS
GNLFHVAWQGNFEAWVQDPFHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNNAYSGVYQ
WWYTIGLRTNEDLYTGAIFLLFLSFISLLAGWLHLQPKWKPSVSWFKNAESRLNHHLSGL
FGVSSLAWAGHLVHVAIPGSRGEYVRWNNFLDVLPYPQGLGPLLTGQWNLYAQNPSSSNH
LFGTTQGAGTAILTILGGFHPQTQSLWLTDMAHHHLAIAFLFLIGGLMYRTNFGIGHSIK
YILEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAFIA
QDFTTQAALYTHHQYIAGFIMTGAFAHGPIFFIRDYNPEQNADNVLARMLEHKEAIISHL
SWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSSTN
SPALNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDAR
GSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDDFYLAVFWMLNTIGWVTFYWHWKHITLW
QGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYTPLVCNSLSVWAWMFLFGHLVWATGFM
FLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVALSIVQARLVGLVHFSVGYIFTYA
AFLIASTSGKF
Sequence of entity 3 (C), FASTA
>4RKU_3 Photosystem I iron-sulfur center (chains C)
SHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPTD
FLSVRVYLWHETTRSMGLAY
Sequence of entity 4 (D), FASTA
>4RKU_4 Photosystem I reaction center subunit II, chloroplastic (chains D)
TPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLL
KLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGVNFR
SIGKNVSPIEVKFTGKQ
Sequence of entity 5 (E), FASTA
>4RKU_5 Photosystem I reaction center subunit IV B, chloroplastic (chains E)
PIGPKRGAKVKILRQESYWYKGTGSVVTVDQDPNTRYPVVVRFNKVNYANVSTNNYALDE
VEE
Sequence of entity 6 (F), FASTA
>4RKU_6 Photosystem I reaction center subunit III, chloroplastic (chains F)
SGLTPCKESKQFAKREKQSIKKLESSLKIYAADSAPALAINATIEKTKRRFDNYAKQGLL
CGADGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDEKKPTQKEIIID
VPLASRLVFRGFSWPIAAYRELLNGELVAKDV
Sequence of entity 7 (G), FASTA
>4RKU_7 Photosystem I reaction center subunit V, chloroplastic (chains G)
PSLVISLSTGLSLFLGRFVFFNFQRENVAKQVPEQNGKGTHFDAGDERAKEYAGLLKSAA
AIVDVLAWGSIGHIVAYYLALTTS
Sequence of entity 8 (H), FASTA
>4RKU_8 Photosystem I reaction center subunit VI, chloroplastic (chains H)
YFDLEDIGNTTGQWDLYGSDAPSPYSPLQSKFFETFAAPFTKRGLLLKFLILGGGSTLAY
FSTTASGDILPIVKGPQLPPKL
Sequence of entity 9 (I), FASTA
>4RKU_9 Photosystem I reaction center subunit VIII (chains I)
PSLFVPLVGLLFPAVAMASLFLHVEK
Sequence of entity 10 (J), FASTA
>4RKU_10 Photosystem I reaction center subunit IX (chains J)
RDLKTYLSVAPVASTLWFAALAGLLIEINRLFPDALTFPF
Sequence of entity 11 (K), FASTA
>4RKU_11 Photosystem I reaction center subunit X psaK (chains K)
DFIGSSTNVIMVASTTLMLFAGRFGLAPSANRKATAGLKLEARDSGLQTGDPAGFTLADT
LACGTVGHIIGV
Sequence of entity 12 (L), FASTA
>4RKU_12 Photosystem I reaction center subunit XI, chloroplastic (chains L)
SEKPTYQVVQPINGDPFIGSLETPVTSSPLVAWYLSNLPGYRTAVNPLLRGIEVGLAHGF
FLVGPFVKAGPLRNTEYAGAAGSLAAAGLVVILSICLTIYGISSFNEGDPSTAPSLTLTG
RKKQPDQLQTADGWAKFTGGFFFGGISGVIWAFFLLYVLDLPY
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| BCR | Beta-carotene | C40 H56 | 21 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 5 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 157 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| CL0 | Chlorophyll a isomer | C55 H72 Mg N4 O5 | 1 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 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 | 6 |
| NEX | (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimeth… | C40 H56 O4 | 1 |
| G3P | Sn-glycerol-3-phosphate | C3 H9 O6 P | 1 |
Primary citation
Crystal structure of plant Photosystem I at 3.1 Angstrom resolution. Mazor, Y., Borovikova, A., Greenberg, I. et al. To be published.
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
- 4Y28 2.8 Å, The structure of plant photosystem I super-complex at 2.8 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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