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Crystal structure of plant Photosystem I at 3 Angstrom resolution

X-ray diffraction
3Å resolution
PDB entry 4rku coloured by chain, front view.
PDB entry 4rku coloured by chain, side view.
PDB entry 4rku coloured by chain, top view.
Source organism: Pisum sativum
Assembly composition:
hetero heptadecamer (preferred)
Entry contents: 17 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Photosystem I
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Multimeric state: hetero heptadecamer
Accessible surface area: 136294.35 Å2
Buried surface area: 277047.62 Å2
Dissociation area: 3,187.88 Å2
Dissociation energy (ΔGdiss): -10.1 kcal/mol
Dissociation entropy (TΔSdiss): 30.48 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-101377

Macromolecules

Photosystem I P700 chlorophyll a apoprotein A1
Chain: A
Length: 721 amino acids
Theoretical weight: 80.08 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P05310 (Residues: 38-758; Coverage: 95%)
Gene names: psaA, psaA1
Pfam: Photosystem I psaA/psaB protein
InterPro:
CATH: Photosystem I PsaA/PsaB
Photosystem I P700 chlorophyll a apoprotein A1 in PDB entry 4rku, assembly 1, front view.
Photosystem I P700 chlorophyll a apoprotein A1 in PDB entry 4rku, assembly 1, side view.
Photosystem I P700 chlorophyll a apoprotein A1 in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P05310  
1721100200300400500600700
 
200400600GHFSRTIAKGPDTTTWIWNLHADAHDFDSHTSDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLNDPTHIRPSAQVVWPIVGQEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAGLMLFAGWFHYHKAAPKLAWFQDVESMLNHHLAGLLGLGSLSWARHQVHVSLPINQFLNAGVDPKEIPLPHEFILNRDLLAQLYPSFAEGATPFFTLNWSKYADFLTFRGGLDPLTGGLWLTDIAHHHLAIAILFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSINLAMLGSLTIVVAQHMYSMPPYPYLATDYATQLSLFTHHMWIGGFLIVGAAAHAAIFMVRDYDPTTRYNDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVFAQWIQNTHALAPGTTAPGATASTSLTWGGGDLVAVGNKVALLPIPLGTADFLVHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSISVVIFHFSWKMQSDVWGSINDQGVVTHITGGNFAQSSITINGWLRDFLWAQASQVIQSYGSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSIVQGRAVGVTHYLLGGIATTWAFFLARIIAVG
UniProt
P05310
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Domains
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Photosystem I P700 chlorophyll a apoprotein A2
Chain: B
Length: 731 amino acids
Theoretical weight: 82.28 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P05311 (Residues: 3-733; Coverage: 100%)
Gene names: psaA2, psaB
Pfam: Photosystem I psaA/psaB protein
InterPro:
CATH: Photosystem I PsaA/PsaB
Photosystem I P700 chlorophyll a apoprotein A2 in PDB entry 4rku, assembly 1, front view.
Photosystem I P700 chlorophyll a apoprotein A2 in PDB entry 4rku, assembly 1, side view.
Photosystem I P700 chlorophyll a apoprotein A2 in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P05311  
1731100200300400500600700
 
200400600LRIPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEGRLYQNIFASHFGQLAIIFLWTSGNLFHVAWQGNFEAWVQDPFHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNNAYSGVYQWWYTIGLRTNEDLYTGAIFLLFLSFISLLAGWLHLQPKWKPSVSWFKNAESRLNHHLSGLFGVSSLAWAGHLVHVAIPGSRGEYVRWNNFLDVLPYPQGLGPLLTGQWNLYAQNPSSSNHLFGTTQGAGTAILTILGGFHPQTQSLWLTDMAHHHLAIAFLFLIGGLMYRTNFGIGHSIKYILEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAFIAQDFTTQAALYTHHQYIAGFIMTGAFAHGPIFFIRDYNPEQNADNVLARMLEHKEAIISHLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSSTNSPALNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDDFYLAVFWMLNTIGWVTFYWHWKHITLWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYTPLVCNSLSVWAWMFLFGHLVWATGFMFLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVALSIVQARLVGLVHFSVGYIFTYAAFLIASTSGKF
UniProt
P05311
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Photosystem I iron-sulfur center
Chain: C
Length: 80 amino acids
Theoretical weight: 8.86 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P10793 (Residues: 2-81; Coverage: 99%)
Gene names: frxA, psaC
Pfam: 4Fe-4S dicluster domain
InterPro:
CATH: Alpha-Beta Plaits
Photosystem I iron-sulfur center in PDB entry 4rku, assembly 1, front view.
Photosystem I iron-sulfur center in PDB entry 4rku, assembly 1, side view.
Photosystem I iron-sulfur center in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P10793  
1801020304050607080
 
20406080SHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY
UniProt
P10793
Chains
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Photosystem I reaction center subunit II, chloroplastic
Chain: D
Length: 137 amino acids
Theoretical weight: 15.35 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K8 (Residues: 1-134; Coverage: 97%)
Pfam: PsaD
InterPro:
CATH: Photosystem I PsaD, reaction center subunit II
Photosystem I reaction center subunit II, chloroplastic in PDB entry 4rku, assembly 1, front view.
Photosystem I reaction center subunit II, chloroplastic in PDB entry 4rku, assembly 1, side view.
Photosystem I reaction center subunit II, chloroplastic in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: E1C9K8  
1137102030405060708090100110120130
 
50100TPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGVNFRSIGKNVSPIEVKFTGKQ
UniProt
E1C9K8
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Photosystem I reaction center subunit IV
Chain: E
Length: 63 amino acids
Theoretical weight: 7.18 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K6 (Residues: 1-62; Coverage: 97%)
Pfam: Photosystem I reaction centre subunit IV / PsaE
InterPro:
CATH: SH3 type barrels.
Photosystem I reaction center subunit IV in PDB entry 4rku, assembly 1, front view.
Photosystem I reaction center subunit IV in PDB entry 4rku, assembly 1, side view.
Photosystem I reaction center subunit IV in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: E1C9K6  
16351015202530354045505560
 
204060PIGPKRGAKVKILRQESYWYKGTGSVVTVDQDPNTRYPVVVRFNKVNYANVSTNNYALDEVEE
UniProt
E1C9K6
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Photosystem I reaction center subunit III
Chain: F
Length: 152 amino acids
Theoretical weight: 17.03 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: A0A0H2UKZ4 (Residues: 1-152; Coverage: 100%)
Pfam: Photosystem I reaction centre subunit III
InterPro:
CATH: Photosystem I PsaF, reaction centre subunit III
Photosystem I reaction center subunit III in PDB entry 4rku, assembly 1, front view.
Photosystem I reaction center subunit III in PDB entry 4rku, assembly 1, side view.
Photosystem I reaction center subunit III in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0A0H2UKZ4  
115220406080100120140
 
50100150SGLTPCKESKQFAKREKQSIKKLESSLKIYAADSAPALAINATIEKTKRRFDNYAKQGLLCGADGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDEKKPTQKEIIIDVPLASRLVFRGFSWPIAAYRELLNGELVAKDV
UniProt
A0A0H2UKZ4
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Photosystem I reaction center subunit V
Chain: G
Length: 84 amino acids
Theoretical weight: 9.08 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P20120 (Residues: 4-39; Coverage: 90%)
Gene name: PSAG
Pfam: Photosystem I psaG / psaK
InterPro:
Photosystem I reaction center subunit V in PDB entry 4rku, assembly 1, front view.
Photosystem I reaction center subunit V in PDB entry 4rku, assembly 1, side view.
Photosystem I reaction center subunit V in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P20120  
1841020304050607080
 
20406080PSLVISLSTGLSLFLGRFVFFNFQRENVAKQVPEQNGKGTHFDAGDERAKEYAGLLKSAAAIVDVLAWGSIGHIVAYYLALTTS
UniProt
P20120
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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Photosystem I reaction center subunit VI
Chain: H
Length: 82 amino acids
Theoretical weight: 8.9 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K9 (Residues: 1-69; Coverage: 100%)
Pfam: Photosystem I reaction centre subunit VI
InterPro: Photosystem I PsaH, reaction centre subunit VI
Photosystem I reaction center subunit VI in PDB entry 4rku, assembly 1, front view.
Photosystem I reaction center subunit VI in PDB entry 4rku, assembly 1, side view.
Photosystem I reaction center subunit VI in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: E1C9K9  
1821020304050607080
 
20406080YFDLEDIGNTTGQWDLYGSDAPSPYSPLQSKFFETFAAPFTKRGLLLKFLILGGGSTLAYFSTTASGDILPIVKGPQLPPKL
UniProt
E1C9K9
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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Photosystem I reaction center subunit VIII
Chain: I
Length: 26 amino acids
Theoretical weight: 2.8 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: P17227 (Residues: 5-30; Coverage: 65%)
Gene name: psaI
Pfam: Photosystem I reaction centre subunit VIII
InterPro:
Photosystem I reaction center subunit VIII in PDB entry 4rku, assembly 1, front view.
Photosystem I reaction center subunit VIII in PDB entry 4rku, assembly 1, side view.
Photosystem I reaction center subunit VIII in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P17227  
1262468101214161820222426
 
1020PSLFVPLVGLLFPAVAMASLFLHVEK
UniProt
P17227
Chains
Domains
Secondary structure
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Early folding residue predictions
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Sequence conservation
Molecule details ›

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Photosystem I reaction center subunit IX
Chain: J
Length: 40 amino acids
Theoretical weight: 4.46 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: D5MAL3 (Residues: 2-41; Coverage: 95%)
Gene name: psaJ
Pfam: Photosystem I reaction centre subunit IX / PsaJ
InterPro:
CATH: Single helix bin
Photosystem I reaction center subunit IX in PDB entry 4rku, assembly 1, front view.
Photosystem I reaction center subunit IX in PDB entry 4rku, assembly 1, side view.
Photosystem I reaction center subunit IX in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: D5MAL3  
140510152025303540
 
10203040RDLKTYLSVAPVASTLWFAALAGLLIEINRLFPDALTFPF
UniProt
D5MAL3
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Domains
Secondary structure
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PSI-K
Chain: K
Length: 72 amino acids
Theoretical weight: 7.26 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L3 (Residues: 1-72; Coverage: 86%)
Pfam: Photosystem I psaG / psaK
InterPro:
PSI-K in PDB entry 4rku, assembly 1, front view.
PSI-K in PDB entry 4rku, assembly 1, side view.
PSI-K in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: E1C9L3  
17210203040506070
 
204060DFIGSSTNVIMVASTTLMLFAGRFGLAPSANRKATAGLKLEARDSGLQTGDPAGFTLADTLACGTVGHIIGV
UniProt
E1C9L3
Chains
Domains
Secondary structure
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Interaction interfaces
Sequence conservation
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PSI subunit V
Chain: L
Length: 163 amino acids
Theoretical weight: 17.31 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L1 (Residues: 1-161; Coverage: 100%)
Pfam: Photosystem I reaction centre subunit XI
InterPro:
CATH: Photosystem I PsaL, reaction centre subunit XI
PSI subunit V in PDB entry 4rku, assembly 1, front view.
PSI subunit V in PDB entry 4rku, assembly 1, side view.
PSI subunit V in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: E1C9L1  
116320406080100120140160
 
50100150SEKPTYQVVQPINGDPFIGSLETPVTSSPLVAWYLSNLPGYRTAVNPLLRGIEVGLAHGFFLVGPFVKAGPLRNTEYAGAAGSLAAAGLVVILSICLTIYGISSFNEGDPSTAPSLTLTGRKKQPDQLQTADGWAKFTGGFFFGGISGVIWAFFLLYVLDLPY
UniProt
E1C9L1
Chains
Domains
Secondary structure
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Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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Photosystem I-N subunit
Chain: N
Length: 85 amino acids
Theoretical weight: 9.74 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9K7 (Residues: 1-85; Coverage: 100%)
Pfam: Photosystem I reaction centre subunit N (PSAN or PSI-N)
InterPro:
Photosystem I-N subunit in PDB entry 4rku, assembly 1, front view.
Photosystem I-N subunit in PDB entry 4rku, assembly 1, side view.
Photosystem I-N subunit in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: E1C9K7  
1851020304050607080
 
20406080SVFDAYLEKSKANKELNDKKRLATSGANFARAYTVQFGTCKFPENFTGCQDLAKQKKVPFISEDLELECEGKDKFKCGSNVFWKW
UniProt
E1C9K7
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Interaction interfaces
Sequence conservation
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Chlorophyll a-b binding protein, chloroplastic
Chain: 1
Length: 182 amino acids
Theoretical weight: 20.1 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: E1C9L2 (Residues: 1-170; Coverage: 100%)
Pfam: Chlorophyll A-B binding protein
InterPro:
Chlorophyll a-b binding protein, chloroplastic in PDB entry 4rku, assembly 1, front view.
Chlorophyll a-b binding protein, chloroplastic in PDB entry 4rku, assembly 1, side view.
Chlorophyll a-b binding protein, chloroplastic in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: E1C9L2  
118220406080100120140160180
 
50100150PRPSYLDGSAPGDFGFDPLRLGEVPENLERFKESELIHCRWAMLAVPGILVPEALGLGNWVKAQEWAALPGGQATYLGNPVPWGTLPTILVIEFLSIAFVEHQRSMEKDPEKKKYPGGAFDPLGYSKDPKKFHEYKIKEVKNGRLALLAFVGICVQQSAYPGTGPLENLATHLADPWHNNIG
UniProt
E1C9L2
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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Chlorophyll a-b binding protein, chloroplastic
Chain: 2
Length: 199 amino acids
Theoretical weight: 21.97 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q41038 (Residues: 59-257; Coverage: 74%)
Gene names: KIW84_045602, lhaB
Pfam: Chlorophyll A-B binding protein
InterPro:
Chlorophyll a-b binding protein, chloroplastic in PDB entry 4rku, assembly 1, front view.
Chlorophyll a-b binding protein, chloroplastic in PDB entry 4rku, assembly 1, side view.
Chlorophyll a-b binding protein, chloroplastic in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q41038  
119920406080100120140160180
 
50100150200VAEPDRPLWFPGSTPPPWLDGSLPGDFGFDPLGLGSDPESLRWNVQAELVHSRWAMLGAAGIFIPEFLTKLGILNTPSWYTAGEQEYFTDTTTLFIVELVFIGWAEGRRWADILNPGCVNTDPIFPNNKLTGTDVGYPGGLWFDPLGWGSASPQKLKELRTKEIKNGRLAMLAVMGAWFQHIYTGTGPIDNLFAHLADP
UniProt
Q41038
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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Chlorophyll a-b binding protein 3, chloroplastic
Chain: 3
Length: 275 amino acids
Theoretical weight: 29.63 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q32904 (Residues: 1-275; Coverage: 100%)
Gene name: lhca3
Pfam: Chlorophyll A-B binding protein
InterPro:
Chlorophyll a-b binding protein 3, chloroplastic in PDB entry 4rku, assembly 1, front view.
Chlorophyll a-b binding protein 3, chloroplastic in PDB entry 4rku, assembly 1, side view.
Chlorophyll a-b binding protein 3, chloroplastic in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q32904  
127520406080100120140160180200220240260
 
100200MATQALVSSSSLTFAAEAVRQSFRARSLPSSVGCSRKGLVRAAATPPVKQGGVDRPLWFASKQSLSYLDGSLPGDYGFDPLGLSDPEGTGGFIEPRWLAYGEVINGRFAMLGAVGAIAPEYLGKVGLIPQETALAWFQTGVIPPAGTYNYWADNYTLFVLEMALMGFAEHRRFQDWAKPGSMGKQYFLGLEKGFGGSGNPAYPGGPFFNPLGFGKDEKSLKELKLKEVKNGRLAMLAILGYFIQGLVTGVGPYQNLLDHVADPVNNNVLTSLKFH
UniProt
Q32904
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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Chlorophyll a-b binding protein P4, chloroplastic
Chain: 4
Length: 196 amino acids
Theoretical weight: 21.78 KDa
Source organism: Pisum sativum
UniProt:
  • Canonical: Q9SQL2 (Residues: 53-248; Coverage: 78%)
Gene name: lhcA-P4
Pfam: Chlorophyll A-B binding protein
InterPro:
Chlorophyll a-b binding protein P4, chloroplastic in PDB entry 4rku, assembly 1, front view.
Chlorophyll a-b binding protein P4, chloroplastic in PDB entry 4rku, assembly 1, side view.
Chlorophyll a-b binding protein P4, chloroplastic in PDB entry 4rku, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q9SQL2  
119620406080100120140160180
 
50100150KGEWLPGLASPGYLTGSLPGDNGFDPLGLAEDPENLRWFVQAELVNGRWAMLGVAGMLLPEVFTSIGIINVPKWYDAGKEEYFASSSTLFVIEFILFHYVEIRRWQDIKNPGSVNQDPIFKQYSLPAGEVGYPGGIFNPLNFAPTLEAKEKEIANGRLAMLAFLGFIIQHNVTGKGPFDNLLQHISDPWHNTIVQT
UniProt
Q9SQL2
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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