7VD6

Structure of S1M1-type FCPII complex from diatom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex

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

(2022) Nat Commun 13: 1764


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a/b-binding proteinA [auth 11],
C [auth 13],
D [auth 14],
E [auth 15],
H [auth 18]
207Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A679BXP6 (Chaetoceros neogracilis)
Explore A0A679BXP6 
Go to UniProtKB:  A0A679BXP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A679BXP6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fcpb2, Fucoxanthin chlorophyll a/c-binding proteinB [auth 12]207Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fcpb3, Fucoxanthin chlorophyll a/c-binding proteinF [auth 16]210Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fcpb4, Fucoxanthin chlorophyll a/c-binding proteinG [auth 17]207Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fcpb5, Fucoxanthin chlorophyll a/c-binding proteinI [auth 19]271Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Fcpb6, Fucoxanthin chlorophyll a/c-binding proteinJ [auth 20]223Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Fcpb7, Fucoxanthin chlorophyll a/c-binding proteinK [auth 21]195Chaetoceros neogracilisMutation(s): 0 
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AG [auth 20]
BB [auth 13]
BD [auth 16]
BG [auth 20]
CG [auth 20]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

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MD [auth 16],
QD [auth 17]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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AA [auth 11],
HE [auth 17],
ND [auth 16],
Z [auth 11]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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GE [auth 17],
IG [auth 21],
RF [auth 19],
YG [auth 21]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
Query on A86

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AC [auth 14]
AE [auth 17]
BC [auth 14]
BE [auth 17]
CA [auth 11]
(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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AB [auth 13]
AD [auth 16]
CB [auth 13]
CD [auth 16]
DD [auth 16]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6
Query on DD6

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FG [auth 20]
HG [auth 20]
KD [auth 16]
PF [auth 19]
TG [auth 21]
(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
LMU
Query on LMU

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SF [auth 19]DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
UNL
Query on UNL

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AF [auth 18]
BA [auth 11]
BF [auth 18]
CF [auth 18]
DF [auth 18]
Unknown ligand
NLEBIOOXCVAHBD-YHBSTRCHSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection, Refinement description