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


This is version 1.0 of the entry. See complete history


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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1751Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II139Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV67Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III185Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]36Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]41Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII [auth L]151Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIJ [auth M]30Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 1K [auth 1u]130Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit Psa28L [auth 2u]121Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr15M [auth 1]227Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr8N [auth 2]205Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr2O [auth 3]200Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr9P [auth 4]215Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr11Q [auth 5]266Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr12R [auth 6]208Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr10S [auth 7]296Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr4T [auth 8]270Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcf6U [auth 9]214Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr3V [auth 10]207Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq13W [auth 11]229Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq3X [auth 12]204Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq11Y [auth 13]244Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq10Z [auth 14]249Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq8AA [auth 15]281Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq5BA [auth 16]218Chaetoceros neogracilisMutation(s): 0 
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AB [auth A]
AD [auth B]
AG [auth 2]
AH [auth 4]
AI [auth 5]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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CA [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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AP [auth 14]
BE [auth B]
BF [auth 2u]
DE [auth B]
FC [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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BC [auth A]
CC [auth A]
CE [auth B]
DJ [auth 6]
GI [auth 5]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
Query on A86

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AF [auth 2u]
BJ [auth 6]
BM [auth 10]
CF [auth 2u]
CM [auth 10]
(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
KC1
Query on KC1

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AN [auth 12]
AO [auth 13]
BG [auth 2]
BI [auth 5]
BO [auth 13]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6
Query on DD6

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AJ [auth 6]
AM [auth 10]
CG [auth 2]
CI [auth 5]
CJ [auth 6]
(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
BCR
Query on BCR

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AC [auth A]
AE [auth B]
ME [auth F]
OE [auth I]
QE [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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BP [auth 15]
DC [auth A]
EC [auth A]
EE [auth B]
EJ [auth 7]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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UB [auth A],
UD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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HE [auth C],
IE [auth C],
VB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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