6J3Y

Structure of C2S2-type PSII-FCPII supercomplex from diatom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.

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

(2019) Nat Plants 5: 890-901

  • DOI: https://doi.org/10.1038/s41477-019-0477-x
  • Primary Citation of Related Structures:  
    6J3Y, 6J3Z, 6J40

  • PubMed Abstract: 

    Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. Diatoms are one of the important groups of oxyphototrophs and possess fucoxanthin chlorophyll a/c-binding proteins (FCPs) as light harvesters. The organization and association pattern of FCP with the photosystem II (PSII) core are unknown. Here we solved the structure of PSII-FCPII supercomplexes isolated from a diatom, Chaetoceros gracilis, by single-particle cryoelectron microscopy. The PSII-FCPII forms a homodimer. In each monomer, two FCP homotetramers and three FCP monomers are associated with one PSII core. The structure reveals a highly complicated protein-pigment network that is different from the green-type light-harvesting apparatus. Comparing these two systems allows the identification of energy transfer and quenching pathways. These findings provide structural insights into not only excitation-energy transfer mechanisms in the diatom PSII-FCPII, but also changes of light harvesters between the red- and green-lineage oxyphototrophs during evolution.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein D1A,
Y [auth a]
344Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II chlorophyll protein CP47B,
Z [auth b]
509Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II chlorophyll protein CP43AA [auth c],
C
471Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein D2BA [auth d],
D
351Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaCA [auth e],
E
84Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaDA [auth f],
F
43Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HEA [auth h],
G [auth H]
67Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B7XBY7 (Chaetoceros neogracilis)
Explore B7XBY7 
Go to UniProtKB:  B7XBY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7XBY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IFA [auth i],
H [auth I]
38Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JGA [auth j],
I [auth J]
39Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KHA [auth k],
J [auth K]
44Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LIA [auth l],
K [auth L]
38Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MJA [auth m],
L [auth M]
131Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIKA [auth o],
M [auth O]
248Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6ZHE8 (Chaetoceros neogracilis)
Explore B6ZHE8 
Go to UniProtKB:  B6ZHE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZHE8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TLA [auth t],
N [auth T]
31Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIMA [auth u],
O [auth U]
93Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6ZHF0 (Chaetoceros neogracilis)
Explore B6ZHF0 
Go to UniProtKB:  B6ZHF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZHF0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550NA [auth v],
P [auth V]
137Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6ZHF4 (Chaetoceros neogracilis)
Explore B6ZHF4 
Go to UniProtKB:  B6ZHF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZHF4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12OA [auth y],
Q [auth Y]
34Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinPA [auth x],
R [auth X]
38Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6ZHF2 (Chaetoceros neogracilis)
Explore B6ZHF2 
Go to UniProtKB:  B6ZHF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZHF2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZQA [auth z],
S [auth Z]
61Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIRA [auth q],
T [auth Q]
155Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6ZHE9 (Chaetoceros neogracilis)
Explore B6ZHE9 
Go to UniProtKB:  B6ZHE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZHE9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein WSA [auth w],
U [auth W]
72Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 0TA [auth 5],
V [auth 0]
31Chaetoceros neogracilisMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 1UA [auth 6],
W [auth 1]
30Chaetoceros neogracilisMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 2VA [auth 7],
X [auth 2]
10Chaetoceros neogracilisMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1207Chaetoceros neogracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
AD [auth C]
AG [auth c]
BD [auth C]
NG [auth h]
OG [auth j]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AC [auth B]
AF [auth b]
AH [auth w]
AI [auth 12]
AL [auth 33]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

Download Ideal Coordinates CCD File 
EG [auth d],
FE [auth a],
GB [auth A],
GD [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

Download Ideal Coordinates CCD File 
FF [auth b]
GC [auth B]
IE [auth a]
JB [auth A]
PG [auth l]
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

Download Ideal Coordinates CCD File 
AE [auth W]
CD [auth C]
DF [auth b]
EC [auth B]
EF [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

Download Ideal Coordinates CCD File 
FG [auth d],
HD [auth D],
IG [auth d],
KD [auth D]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
GF [auth b]
HC [auth B]
KE [auth a]
LB [auth A]
QG [auth l]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
Query on A86

Download Ideal Coordinates CCD File 
AJ [auth 14]
AK [auth 31]
AM [auth 34]
BK [auth 31]
BM [auth 34]
(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
HEM
Query on HEM

Download Ideal Coordinates CCD File 
LG [auth f],
MD [auth E],
VG [auth v],
XD [auth V]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

Download Ideal Coordinates CCD File 
BF [auth b]
BG [auth c]
CC [auth B]
CF [auth b]
DC [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

Download Ideal Coordinates CCD File 
HK [auth 32],
TH [auth 12]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
OEX
Query on OEX

Download Ideal Coordinates CCD File 
JF [auth c],
KC [auth C]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
JE [auth a],
KB [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

Download Ideal Coordinates CCD File 
DE [auth a],
EB [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13_2998
RECONSTRUCTIONRELION2.1

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other