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

ElementResiduesLengthSheet
α-helix67-7610
α-helix77-9620
α-helix134-15320
α-helix187-19711
α-helix198-2025
α-helix203-2042
Chain 2: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix104-12623
α-helix127-1293
α-helix151-17222
α-helix218-24124
Chain 3: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix97-11014
α-helix161-17515
α-helix227-2337
α-helix236-2427
Chain 4: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix89-10820
α-helix141-16121
α-helix180-1834
α-helix203-22119
Chain A: 39 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix251
α-helix32-332
α-helix52-554
β-strand5611
β-strand5911
α-helix74-8916
α-helix91-10010
α-helix106-1116
β-strand119-12132
β-strand143-14422
α-helix153-1553
α-helix161-1644
α-helix167-1737
α-helix183-1875
α-helix194-1974
α-helix203-2064
α-helix207-2115
α-helix216-2194
α-helix228-2303
α-helix298-31114
β-strand312-31323
α-helix328-3314
α-helix341-3433
α-helix349-3524
α-helix356-36712
α-helix372-3776
α-helix389-3924
α-helix394-40512
α-helix409-41911
α-helix431-4377
α-helix447-4559
α-helix459-4646
α-helix465-4695
α-helix493-4964
α-helix541-56121
α-helix600-62223
α-helix630-6323
α-helix642-6443
α-helix6511
α-helix652-6576
α-helix686-6938
α-helix698-71316
α-helix728-7325
α-helix736-75015
Chain B: 35 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix11-144
α-helix19-246
α-helix39-479
α-helix52-6615
α-helix121-1244
α-helix139-1468
α-helix148-1558
α-helix166-1694
β-strand17214
β-strand17514
α-helix178-1814
α-helix183-19614
α-helix199-2024
α-helix204-2063
α-helix224-2263
α-helix272-28716
β-strand29115
β-strand29915
β-strand31816
α-helix322-3276
α-helix333-3364
α-helix341-35111
α-helix381-3899
α-helix400-4034
β-strand40616
α-helix415-4184
α-helix423-44321
β-strand45517
α-helix458-4625
α-helix516-5227
α-helix526-53914
α-helix573-5797
α-helix586-5938
α-helix599-6024
α-helix607-6126
α-helix629-6324
α-helix645-65814
α-helix662-6654
α-helix669-67810
α-helix682-6843
α-helix704-7085
α-helix713-72614
Chain D: 2 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand10118
β-strand102-10329
β-strand111-112210
β-strand120-121210
β-strand13018
α-helix135-1428
α-helix143-1453
β-strand153-15429
Chain E: 0 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand74111
β-strand88111
β-strand89-90212
β-strand104113
β-strand105-106212
β-strand119113

9 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Photosystem I P700 chlorophyll a apoprotein A1Aprotein738Pisum sativumP05310 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A2Bprotein733Pisum sativumP05311 (AlphaFold model)
Photosystem I iron-sulfur centerCprotein81Pisum sativumP10793 (AlphaFold model)
Putative uncharacterized proteinDprotein138Pisum sativumE1C9K8 (AlphaFold model)
Putative uncharacterized proteinEprotein64Pisum sativumE1C9K6
Photosystem I reaction center subunit III, chloroplasticFprotein154Pisum sativumP12355
Putative uncharacterized proteinGprotein95Pisum sativumP20120
Putative uncharacterized proteinHprotein69Pisum sativumE1C9K9
Photosystem I reaction center subunit VIIIIprotein30Pisum sativumP17227
Photosystem I reaction center subunit IXJprotein42Pisum sativumE1C9L0
Photosystem I reaction center subunit X psaKKprotein84Pisum sativumE1C9L3
Putative uncharacterized proteinLprotein161Pisum sativumE1C9L1

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

IDNameFormulaCopies
LMG1,2-distearoyl-monogalactosyl-diglycerideC45 H86 O101
SF4Iron/sulfur clusterFe4 S43
LMUDodecyl-alpha-D-maltosideC24 H46 O1153
BCRBeta-caroteneC40 H5619
PQNPhylloquinoneC31 H46 O22
CLAChlorophyll aC55 H72 Mg N4 O5174

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:

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