6J40

Structure of C2S2M2-type PSII-FCPII supercomplex from diatom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 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: 10.1038/s41477-019-0477-x
  • Primary Citation of Related Structures:  

  • 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 oxyphot ...

    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

    National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi, Japan.,Graduate School of Science, Kobe University, Hyogo, Japan.,Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.,Japan Science and Technology Agency, PRESTO, Saitama, Japan. fusamichi_a@okayama-u.ac.jp.,Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan. shen@okayama-u.ac.jp.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan. fusamichi_a@okayama-u.ac.jp.,Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, Japan. naomiyazaki@tara.tsukuba.ac.jp.,Institute for Protein Research, Osaka University, Osaka, Japan. naomiyazaki@tara.tsukuba.ac.jp.,Graduate School of Life Science, University of Hyogo, Hyogo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein D1
A, a
344N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II chlorophyll protein CP47
B, b
509N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II chlorophyll protein CP43
C, c
471N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein D2
D, d
351N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
84N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
43N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
67Chaetoceros gracilisMutation(s): 0 
Gene Names: psbH
Find proteins for B7XBY7 (Chaetoceros gracilis)
Go to UniProtKB:  B7XBY7
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
38N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
39N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
44N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
38N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
M, m
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Extrinsic protein in photosystem II
O, o
248Chaetoceros gracilisMutation(s): 0 
Gene Names: psbO
Find proteins for B6ZHE8 (Chaetoceros gracilis)
Go to UniProtKB:  B6ZHE8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
31N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Extrinsic protein in photosystem II
U, u
93Chaetoceros gracilisMutation(s): 0 
Gene Names: psbU
Find proteins for B6ZHF0 (Chaetoceros gracilis)
Go to UniProtKB:  B6ZHF0
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Chaetoceros gracilisMutation(s): 0 
Gene Names: psbV
Find proteins for B6ZHF4 (Chaetoceros gracilis)
Go to UniProtKB:  B6ZHF4
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y, y
34N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center X protein
X, x
38Chaetoceros gracilisMutation(s): 0 
Gene Names: psbX
Find proteins for B6ZHF2 (Chaetoceros gracilis)
Go to UniProtKB:  B6ZHF2
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
61N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Extrinsic protein in photosystem II
Q, q
155Chaetoceros gracilisMutation(s): 0 
Gene Names: psbQ'
Find proteins for B6ZHE9 (Chaetoceros gracilis)
Go to UniProtKB:  B6ZHE9
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein W
W, w
72N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown protein 0
0, 5
31N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Unknown protein 1
1, 6
30N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Unknown protein 2
2, 7
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
11, 12, 13, 14, 15, 16, 17, 18, 31, 32, 33, 34, 35, 36, 37, 38
207N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein monomer 1
19, 39
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein monomer 2
20, 40
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Fucoxanthin chlorophyll a/c-binding protein monomer 3
21, 41
155N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

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A, a, B, b, l, L
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
CLA
Query on CLA

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11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, A, a, B, b, c, C, d, D, M, m, w, W, z, Z
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

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d, 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
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
OEX
Query on OEX

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C, c
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
DGD
Query on DGD

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c, C, h, H, J, j
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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12, 32, b, B, c, D, d, M, m, Q, W, w
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCT
Query on BCT

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a, A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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e, E, V, v
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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A, a, B, b, C, c, f, F, H, h, m, Y, Z
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

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Download CCD File 
A, D, d
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
FE2
Query on FE2

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a, A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
A86
Query on A86

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11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41
(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
Fucoxanthin
C42 H58 O6
SJWWTRQNNRNTPU-XJUZQKKNSA-N
 Ligand Interaction
LHG
Query on LHG

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A, a, b, B, d, L, l
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
LMU
Query on LMU

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Download CCD File 
12, 32
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
0, 1, 19, 2, 20, 21, 39, 40, 41, 5, 6, 7
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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