3LW5: Improved model of plant photosystem I
Improved model of plant photosystem I. Determined by X-ray diffraction at 3.3 Å resolution. Released 18 Aug 2010.
- Method
- X-ray diffraction
- Resolution
- 3.3 Å
- Organisms
- Pisum sativum, unidentified
- Chains
- 18
- Atoms
- 36,370
- Mol. weight
- 550.2 kDa
- Ligands
- LMG, SF4, LMU, BCR
- Released
- 18 Aug 2010
Explore 3LW5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3LW5 contains 121 α-helices and 32 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: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 67-76 | 10 | |
| α-helix | 77-96 | 20 | |
| α-helix | 134-153 | 20 | |
| α-helix | 187-197 | 11 | |
| α-helix | 198-202 | 5 | |
| α-helix | 203-204 | 2 | |
Chain 2: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 104-126 | 23 | |
| α-helix | 127-129 | 3 | |
| α-helix | 151-172 | 22 | |
| α-helix | 218-241 | 24 | |
Chain 3: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 97-110 | 14 | |
| α-helix | 161-175 | 15 | |
| α-helix | 227-233 | 7 | |
| α-helix | 236-242 | 7 | |
Chain 4: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 89-108 | 20 | |
| α-helix | 141-161 | 21 | |
| α-helix | 180-183 | 4 | |
| α-helix | 203-221 | 19 | |
Chain A: 39 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25 | 1 | |
| α-helix | 32-33 | 2 | |
| α-helix | 52-55 | 4 | |
| β-strand | 56 | 1 | 1 |
| β-strand | 59 | 1 | 1 |
| α-helix | 74-89 | 16 | |
| α-helix | 91-100 | 10 | |
| α-helix | 106-111 | 6 | |
| β-strand | 119-121 | 3 | 2 |
| β-strand | 143-144 | 2 | 2 |
| α-helix | 153-155 | 3 | |
| α-helix | 161-164 | 4 | |
| α-helix | 167-173 | 7 | |
| α-helix | 183-187 | 5 | |
| α-helix | 194-197 | 4 | |
| α-helix | 203-206 | 4 | |
| α-helix | 207-211 | 5 | |
| α-helix | 216-219 | 4 | |
| α-helix | 228-230 | 3 | |
| α-helix | 298-311 | 14 | |
| β-strand | 312-313 | 2 | 3 |
| α-helix | 328-331 | 4 | |
| α-helix | 341-343 | 3 | |
| α-helix | 349-352 | 4 | |
| α-helix | 356-367 | 12 | |
| α-helix | 372-377 | 6 | |
| α-helix | 389-392 | 4 | |
| α-helix | 394-405 | 12 | |
| α-helix | 409-419 | 11 | |
| α-helix | 431-437 | 7 | |
| α-helix | 447-455 | 9 | |
| α-helix | 459-464 | 6 | |
| α-helix | 465-469 | 5 | |
| α-helix | 493-496 | 4 | |
| α-helix | 541-561 | 21 | |
| α-helix | 600-622 | 23 | |
| α-helix | 630-632 | 3 | |
| α-helix | 642-644 | 3 | |
| α-helix | 651 | 1 | |
| α-helix | 652-657 | 6 | |
| α-helix | 686-693 | 8 | |
| α-helix | 698-713 | 16 | |
| α-helix | 728-732 | 5 | |
| α-helix | 736-750 | 15 | |
Chain B: 35 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-14 | 4 | |
| α-helix | 19-24 | 6 | |
| α-helix | 39-47 | 9 | |
| α-helix | 52-66 | 15 | |
| α-helix | 121-124 | 4 | |
| α-helix | 139-146 | 8 | |
| α-helix | 148-155 | 8 | |
| α-helix | 166-169 | 4 | |
| β-strand | 172 | 1 | 4 |
| β-strand | 175 | 1 | 4 |
| α-helix | 178-181 | 4 | |
| α-helix | 183-196 | 14 | |
| α-helix | 199-202 | 4 | |
| α-helix | 204-206 | 3 | |
| α-helix | 224-226 | 3 | |
| α-helix | 272-287 | 16 | |
| β-strand | 291 | 1 | 5 |
| β-strand | 299 | 1 | 5 |
| β-strand | 318 | 1 | 6 |
| α-helix | 322-327 | 6 | |
| α-helix | 333-336 | 4 | |
| α-helix | 341-351 | 11 | |
| α-helix | 381-389 | 9 | |
| α-helix | 400-403 | 4 | |
| β-strand | 406 | 1 | 6 |
| α-helix | 415-418 | 4 | |
| α-helix | 423-443 | 21 | |
| β-strand | 455 | 1 | 7 |
| α-helix | 458-462 | 5 | |
| α-helix | 516-522 | 7 | |
| α-helix | 526-539 | 14 | |
| α-helix | 573-579 | 7 | |
| α-helix | 586-593 | 8 | |
| α-helix | 599-602 | 4 | |
| α-helix | 607-612 | 6 | |
| α-helix | 629-632 | 4 | |
| α-helix | 645-658 | 14 | |
| α-helix | 662-665 | 4 | |
| α-helix | 669-678 | 10 | |
| α-helix | 682-684 | 3 | |
| α-helix | 704-708 | 5 | |
| α-helix | 713-726 | 14 | |
Chain D: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 101 | 1 | 8 |
| β-strand | 102-103 | 2 | 9 |
| β-strand | 111-112 | 2 | 10 |
| β-strand | 120-121 | 2 | 10 |
| β-strand | 130 | 1 | 8 |
| α-helix | 135-142 | 8 | |
| α-helix | 143-145 | 3 | |
| β-strand | 153-154 | 2 | 9 |
Chain E: 0 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 74 | 1 | 11 |
| β-strand | 88 | 1 | 11 |
| β-strand | 89-90 | 2 | 12 |
| β-strand | 104 | 1 | 13 |
| β-strand | 105-106 | 2 | 12 |
| β-strand | 119 | 1 | 13 |
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 | 738 | Pisum sativum | P05310 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A2 | B | protein | 733 | Pisum sativum | P05311 (AlphaFold model) |
| Photosystem I iron-sulfur center | C | protein | 81 | Pisum sativum | P10793 (AlphaFold model) |
| Putative uncharacterized protein | D | protein | 138 | Pisum sativum | E1C9K8 (AlphaFold model) |
| Putative uncharacterized protein | E | protein | 64 | Pisum sativum | E1C9K6 |
| Photosystem I reaction center subunit III, chloroplastic | F | protein | 154 | Pisum sativum | P12355 |
| Putative uncharacterized protein | G | protein | 95 | Pisum sativum | P20120 |
| Putative uncharacterized protein | H | protein | 69 | Pisum sativum | E1C9K9 |
| Photosystem I reaction center subunit VIII | I | protein | 30 | Pisum sativum | P17227 |
| Photosystem I reaction center subunit IX | J | protein | 42 | Pisum sativum | E1C9L0 |
| Photosystem I reaction center subunit X psaK | K | protein | 84 | Pisum sativum | E1C9L3 |
| Putative uncharacterized protein | L | protein | 161 | Pisum sativum | E1C9L1 |
6 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>3LW5_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
LVDRDPIKTSFEQWAKPGHFSRTIAKGPDTTTWIWNLHADAHDFDSHTSDLEEISRKVFS
AHFGQLSIIFLWLSGMYFHGARFSNYEAWLNDPTHIGPSAQVVWPIVGQEILNGDVGGGF
RGIQITSGFFQIWRASGITSELQLYCTAIGALVFAGLMLFAGWFHYHKAAPKLAWFQDVE
SMLNHHLAGLLGLGSLSWARHQVHVSLPINQFLNAGVDPKEIPLPHEFILNRDLLAQLYP
SFAEGATPFFTLNWSKYADFLTFRGGLDPLTGGLWLTDIAHHHLAIAILFLIAGHMYRTN
WGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSINLAMLGSLTIVVAQHMYSMP
PYPYLATDYATQLSLFTHHMWIGGFLIVGAAAHAAIFMVRDYDPTTRYNDLLDRVLRHRD
AIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVFAQWIQNTHALAP
GTTAPGATASTSLTWGGGDLVAVGNKVALLPIPLGTADFLVHHIHAFTIHVTVLILLKGV
LFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSISVVIFHFSWKM
QSDVWGTINDQGVVTHITAGNFAQSSITINGWLRDFLWAQASQVIQSYGSSLSAYGLFFL
GAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSIVQGRAVGVTHYLL
GGIATTWAFFLARIIAVG
Sequence of entity 2 (B), FASTA
>3LW5_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
ALRIPRFSQGIAQDPTTRRIWFGIATAHDFESHDDITEGRLYQNIFASHFGQLAIIFLWT
SGNLFHVAWQGNFEAWVQDPFHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNNAYSGVY
QWWYTIGLRTNEDLYTGAIFLLFLSFISLLAGWLHLQPKWKPSVSWFKNAESRLNHHLSG
LFGVSSLAWAGHLVHVAIPGSRGEYVRWNNFLDVLPYPQGLGPLLTGQWNLYAQNPSSSN
HLFGTTQGAGTAILTILGGFHPQTQSLWLTDVAHHHLAIAFLFLIGGLMYRTNFGIGHSI
KYILEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAFI
AQDFTTQAALYTHHQYIAGFIMTGAFAHGPIFFIRDYNPEQNADNVLARMLEHKEAIISH
LSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTTYGFDIPLSST
NGPALNAGRNIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDA
RGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDDFYLAVFWMLNTIGWVTFYWHWKHITL
WRGNVSQFNESSTYLMGWLRDYLWLNSSQLINGITPLVCNSLSVWAWMFLFGHLVWATGF
MFLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVALSIVQARLVGLVHFSVGYIFTY
AAFLIASTSGKFG
Sequence of entity 3 (C), FASTA
>3LW5_3 Photosystem I iron-sulfur center (chains C)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY
Sequence of entity 4 (D), FASTA
>3LW5_4 Putative uncharacterized protein (chains D)
ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAIMREGPNLLKLA
RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNAGRQGVGQNFRSIG
KNVSPIEVKFTGKQPYDL
Sequence of entity 5 (E), FASTA
>3LW5_5 Putative uncharacterized protein (chains E)
IGPKRGAKVKILRKESYWYKGTGSVVAVDQDPNTRYPVVVRFNKVNYANVSTNNYALDEI
VEVE
Sequence of entity 6 (F), FASTA
>3LW5_6 Photosystem I reaction center subunit III, chloroplastic (chains F)
DIAGLTPCKESKQFAKREKQALKKLQASLKLYADDSAPALAIKATMEKTKKRFDNYGKYG
LLCGSDGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDEKKPTQKEII
IDVPLASSLLFRGFSWPVAAYRELLNGELVDNNF
Sequence of entity 7 (G), FASTA
>3LW5_7 Putative uncharacterized protein (chains G)
SALVISLSTGLSLFLGRFVFFNFQRENVAKQVPEQNGLTHFEAGDTRAKEYVSLLKSNDP
VGFNIVDVLAWGSIGHVVAYYILATTSNGYDPAFF
Sequence of entity 8 (H), FASTA
>3LW5_8 Putative uncharacterized protein (chains H)
DLEDLGNTTGQWDSYGSDAPSPYNPLQSKLFETFAAPFTKRGLLLKFLILGGGSTLAYLS
ATASGDILP
Sequence of entity 9 (I), FASTA
>3LW5_9 Photosystem I reaction center subunit VIII (chains I)
MINLPSLFVPLVGLLFPAVAMASLFLHVEK
Sequence of entity 10 (J), FASTA
>3LW5_10 Photosystem I reaction center subunit IX (chains J)
MRDLKTYLSVAPVVSTLWFGALAGLLIEINRFFPDALIFPFF
Sequence of entity 11 (K), FASTA
>3LW5_11 Photosystem I reaction center subunit X psaK (chains K)
DFIGSPTNLIMVTSTSLMLFAGRFGLAPSANRKATAGLKLEVRDSGLQTGDPAGFTLADT
LACGVVGHIIGVGVVLGLKNIGAL
Sequence of entity 12 (L), FASTA
>3LW5_12 Putative uncharacterized protein (chains L)
KPTYQVIQPINGDPFIGSLETPVTSSPLIAWYLSNLPAYRTAVSPLLRGIEVGLAHGYLL
VGPFVKAGPLRNTEIAGQAGSLAAGGLVVILSLCLTIYGISSFNEGAPSTAPSLTLTGRK
KEPDQLQTADGWAKFTGGFFFGGISGVIWAYFLLYVLDLPY
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 1 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| LMU | Dodecyl-alpha-D-maltoside | C24 H46 O11 | 53 |
| BCR | Beta-carotene | C40 H56 | 19 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 174 |
Primary citation
Structure determination and improved model of plant photosystem I. Amunts, A., Toporik, H., Borovikova, A. et al. J Biol Chem (2010) 285:3478-3486. DOI 10.1074/jbc.M109.072645 · 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
- 4Y28 2.8 Å, The structure of plant photosystem I 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
- 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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