6L4U

Structure of the PSI-FCPI supercomplex from diatom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structure of photosystem I-light-harvesting supercomplex from a red-lineage diatom

Nagao, R.Kato, K.Ifuku, K.Suzuki, T.Kumazawa, M.Uchiyama, I.Kashino, Y.Dohmae, N.Akimoto, S.Shen, J.R.Miyazaki, N.Akita, F.

(2020) Nat Commun 


Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A2
B
733Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IV
E
67Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit III
F
185Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit VIII
I
36Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit XI
L
151Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Unknown protein 1
1u
130Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit Psa28
2u
121Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcr2
3
200Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcr9
4
215Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcr11
5
266Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcr4
8
270Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcf6
9
214Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcr3
10
207Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcq3
12
204Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcq10
14
249Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcq8
15
281Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A1
A
751Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit XII
M
30Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcr15
1
227Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcr8
2
205Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcr12
6
208Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcr10
7
296Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcq13
11
229Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcq11
13
244Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcq5
16
218Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem I iron-sulfur center
C
81Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit II
D
139Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IX
J
41Chaetoceros gracilisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL0
Query on CL0

Download CCD File 
A
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
 Ligand Interaction
CLA
Query on CLA

Download CCD File 
1, 10, 11, 12, 13, 14, 15, 16, 2, 2u, 3, 4, 5, 6, 7, 8, 9, A, B, F, J, L
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
LMG
Query on LMG

Download CCD File 
14, 2u, 3, 5, 6, 7, 8, A, B, F
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
LHG
Query on LHG

Download CCD File 
2, 5, 6, 9, A, B
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
A86
Query on A86

Download CCD File 
1, 10, 11, 12, 13, 14, 15, 16, 2, 2u, 3, 4, 5, 6, 7, 8, 9
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate
C42 H58 O6
SJWWTRQNNRNTPU-XJUZQKKNSA-N
 Ligand Interaction
KC1
Query on KC1

Download CCD File 
1, 10, 11, 12, 13, 14, 16, 2, 3, 4, 5, 6, 7, 8, 9
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
 Ligand Interaction
DD6
Query on DD6

Download CCD File 
1, 10, 11, 12, 13, 15, 16, 2, 3, 4, 5, 6, 7, 8, 9
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
C40 H54 O3
OGHZCSINIMWCSB-WMTIXGNLSA-N
 Ligand Interaction
BCR
Query on BCR

Download CCD File 
2u, A, B, F, I, J, L, M
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

Download CCD File 
1, 11, 12, 15, 16, 6, 7, 8, 9, A, B
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
PQN
Query on PQN

Download CCD File 
A, B
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
A, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-05-20
    Type: Initial release