7VD6 | pdb_00007vd6

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

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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

Macromolecule Content 

  • Total Structure Weight: 383.71 kDa 
  • Atom Count: 23,937 
  • Modeled Residue Count: 1,916 
  • Deposited Residue Count: 2,348 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  3D Structure
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fcpb2, Fucoxanthin chlorophyll a/c-binding proteinB [auth 12]207Chaetoceros neogracilisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fcpb3, Fucoxanthin chlorophyll a/c-binding proteinF [auth 16]210Chaetoceros neogracilisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Fcpb4, Fucoxanthin chlorophyll a/c-binding proteinG [auth 17]207Chaetoceros neogracilisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Fcpb5, Fucoxanthin chlorophyll a/c-binding proteinI [auth 19]271Chaetoceros neogracilisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Fcpb6, Fucoxanthin chlorophyll a/c-binding proteinJ [auth 20]223Chaetoceros neogracilisMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Fcpb7, Fucoxanthin chlorophyll a/c-binding proteinK [auth 21]195Chaetoceros neogracilisMutation(s): 0 

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA



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AG [auth 20]
BB [auth 13]
BD [auth 16]
BG [auth 20]
CG [auth 20]
AG [auth 20],
BB [auth 13],
BD [auth 16],
BG [auth 20],
CG [auth 20],
DA [auth 12],
DB [auth 13],
DG [auth 20],
EB [auth 13],
ED [auth 16],
EF [auth 19],
FA [auth 12],
FD [auth 16],
FF [auth 19],
GA [auth 12],
GB [auth 13],
GC [auth 15],
GF [auth 19],
HA [auth 12],
HD [auth 16],
HF [auth 19],
IC [auth 15],
IF [auth 19],
JA [auth 12],
JF [auth 19],
JG [auth 21],
KC [auth 15],
KF [auth 19],
L [auth 11],
LA [auth 12],
LG [auth 21],
MC [auth 15],
ME [auth 18],
MF [auth 19],
MG [auth 21],
N [auth 11],
NA [auth 12],
NC [auth 15],
NE [auth 18],
NF [auth 19],
NG [auth 21],
OE [auth 18],
P [auth 11],
PB [auth 14],
PC [auth 15],
PG [auth 21],
QB [auth 14],
QE [auth 18],
QG [auth 21],
R [auth 11],
RB [auth 14],
RD [auth 17],
RG [auth 21],
SE [auth 18],
T [auth 11],
TB [auth 14],
TD [auth 17],
TE [auth 18],
VB [auth 14],
VE [auth 18],
VF [auth 20],
WA [auth 13],
WB [auth 14],
WD [auth 17],
XA [auth 13],
XD [auth 17],
XF [auth 20],
YB [auth 14],
ZA [auth 13],
ZC [auth 16],
ZD [auth 17]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD

Query on SQD



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
AC [auth 14]
AE [auth 17]
BC [auth 14]
BE [auth 17]
CA [auth 11]
AC [auth 14],
AE [auth 17],
BC [auth 14],
BE [auth 17],
CA [auth 11],
CC [auth 14],
CE [auth 17],
DC [auth 14],
DE [auth 17],
EA [auth 12],
EC [auth 14],
EE [auth 17],
EG [auth 20],
FE [auth 17],
GG [auth 20],
HB [auth 13],
IB [auth 13],
ID [auth 16],
JB [auth 13],
JD [auth 16],
KB [auth 13],
KE [auth 17],
LB [auth 13],
LD [auth 16],
OA [auth 12],
OF [auth 19],
PA [auth 12],
QA [auth 12],
QC [auth 15],
QF [auth 19],
RA [auth 12],
RC [auth 15],
SA [auth 12],
SC [auth 15],
SG [auth 21],
TC [auth 15],
U [auth 11],
UC [auth 15],
UF [auth 20],
UG [auth 21],
V [auth 11],
VA [auth 12],
VC [auth 15],
VG [auth 21],
W [auth 11],
WE [auth 18],
WG [auth 21],
X [auth 11],
XE [auth 18],
Y [auth 11],
YC [auth 15],
YE [auth 18],
ZB [auth 14],
ZE [auth 18]
(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]
AB [auth 13],
AD [auth 16],
CB [auth 13],
CD [auth 16],
DD [auth 16],
FB [auth 13],
GD [auth 16],
HC [auth 15],
IA [auth 12],
JC [auth 15],
KA [auth 12],
KG [auth 21],
LC [auth 15],
LF [auth 19],
M [auth 11],
MA [auth 12],
O [auth 11],
OC [auth 15],
OG [auth 21],
PE [auth 18],
Q [auth 11],
RE [auth 18],
S [auth 11],
SB [auth 14],
SD [auth 17],
UB [auth 14],
UD [auth 17],
UE [auth 18],
VD [auth 17],
WF [auth 20],
XB [auth 14],
YA [auth 13],
YD [auth 17],
YF [auth 20],
ZF [auth 20]
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]
FG [auth 20],
HG [auth 20],
KD [auth 16],
PF [auth 19],
TG [auth 21],
XG [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



Download:Ideal Coordinates CCD File
SF [auth 19]DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
UNL

Query on UNL



Download:Ideal Coordinates CCD File
AF [auth 18]
BA [auth 11]
BF [auth 18]
CF [auth 18]
DF [auth 18]
AF [auth 18],
BA [auth 11],
BF [auth 18],
CF [auth 18],
DF [auth 18],
FC [auth 14],
IE [auth 17],
JE [auth 17],
LE [auth 17],
MB [auth 13],
NB [auth 13],
OB [auth 13],
OD [auth 16],
PD [auth 16],
TA [auth 12],
TF [auth 19],
UA [auth 12],
WC [auth 15],
XC [auth 15]
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

View Full Validation Report



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