4YUU

Crystal structure of oxygen-evolving photosystem II from a red alga


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga

Ago, H.Adachi, H.Umena, Y.Tashiro, T.Kawakami, K.Kamiya, N.Tian, L.Han, G.Kuang, T.Liu, Z.Wang, F.Zou, H.Enami, I.Miyano, M.Shen, J.-R.

(2016) J Biol Chem 291: 5676-5687

  • DOI: 10.1074/jbc.M115.711689
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of ...

    Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ', a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ' subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ' were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.


    Related Citations: 
    • Towards structural elucidation of eukaryotic photosystem II: Purification, crystallization and preliminary X-ray diffraction analysis of photosystem II from a red alga.
      Adachi, H., Umena, Y., Enami, I., Henmi, T., Kamiya, N., Shen, J.-R.
      (2009) Biochim Biophys Acta 1787: 121

    Organizational Affiliation

    the Photosynthesis Research Center, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan, the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China, shen@cc.okayama-u.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein D1A1, A2, a1, a2344Cyanidium caldariumMutation(s): 0 
Gene Names: psbA
EC: 1.10.3.9
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19895 (Cyanidium caldarium)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center proteinB1, B2, b1, b2509Cyanidium caldariumMutation(s): 0 
Gene Names: psbB
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19928 (Cyanidium caldarium)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 reaction center proteinC1, C2, c1, c2460Cyanidium caldariumMutation(s): 0 
Gene Names: psbC
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM46 (Cyanidium caldarium)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 proteinD1, D2, d1, d2351Cyanidium caldariumMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM47 (Cyanidium caldarium)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alphaE1, E2, e1, e284Cyanidium caldariumMutation(s): 0 
Gene Names: psbE
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM20 (Cyanidium caldarium)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit betaF1, F2, f1, f243Cyanidium caldariumMutation(s): 0 
Gene Names: psbF
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM21 (Cyanidium caldarium)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein HH1, H2, h1, h267Cyanidium caldariumMutation(s): 0 
Gene Names: psbH
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19925 (Cyanidium caldarium)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein II1, I2, i1, i238Cyanidium caldariumMutation(s): 0 
Gene Names: psbI
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19882 (Cyanidium caldarium)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein JJ1, J2, j1, j239Cyanidium caldariumMutation(s): 0 
Gene Names: psbJ
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM23 (Cyanidium caldarium)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein KK1, K2, k1, k241Cyanidium caldariumMutation(s): 0 
Gene Names: psbK
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TLR0 (Cyanidium caldarium)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein LL1, L2, l1, l238Cyanidium caldariumMutation(s): 0 
Gene Names: psbL
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM22 (Cyanidium caldarium)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM II REACTION CENTER PROTEIN MM1, M2, m1, m2108Cyanidium caldariumMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBOO1, O2, o1, o2329Cyanidium caldariumMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein TT1, T2, t1, t232Cyanidium caldariumMutation(s): 0 
Gene Names: psbT
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19927 (Cyanidium caldarium)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein, chloroplasticU1, U2, u1, u2155Cyanidium caldariumMutation(s): 0 
Gene Names: psbU
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9ZQS5 (Cyanidium caldarium)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550V1, V2, v1, v2155Cyanidium caldariumMutation(s): 0 
Gene Names: psbV
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q76FB0 (Cyanidium caldarium)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12Y1, Y2, y1, y235Cyanidium caldariumMutation(s): 0 
Gene Names: ycf12ycf34
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TLX0 (Cyanidium caldarium)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM II REACTION CENTER PROTEIN XX1, X2, x1, x240Cyanidium caldariumMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE CHAIN UNASSIGNEDS1, S2, s1, s246Cyanidium caldariumMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE CHAIN UNASSIGNEDW1, W2, w1, w225Cyanidium caldariumMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Extrinsic protein in photosystem IIQ2, q1218Cyanidium caldariumMutation(s): 0 
Gene Names: psbQ'
Find proteins for Q76B86 (Cyanidium caldarium)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein ZZ2, z262Cyanidium caldariumMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 17 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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C1, C2, H1, H2, c1, c2, h1, h2
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA
Query on CLA

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A1, A2, B1, B2, C1, C2, D1, D2, K2, a1, a2, b1, b2, c1, c2, d1, d2
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

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A1, A2, D1, D2, a1, a2, d1, d2
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD
Query on SQD

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B2, D1, D2, b2
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
LMG
Query on LMG

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A1, A2, B1, B2, C1, C2, D1, F2, I2, M1, a1, a2, b1, b2, c1, c2, d1, d2, j2
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
PL9
Query on PL9

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D1, D2, d1, d2
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
 Ligand Interaction
LHG
Query on LHG

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A2, B1, B2, D1, D2, L1, L2, a1, a2, b1, b2, d1, d2, l1, l2
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM
Query on HEM

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E1, E2, V1, V2, e2, f1, v1, v2
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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A1, A2, B1, B2, C1, C2, D1, F2, H1, H2, J1, K1, K2, a1, a2, b1, b2, c1, c2, d1, d2, h1, h2, j2, k1, k2, z2
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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C1, L1, M1, T1, a2, b2, c1, i2, l1, m1, m2
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEX
Query on OEX

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A1, A2, a1, a2
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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B1, C1, C2, a1, a2, b1, c1, c2, i1
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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A1, A2, a1, a2
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE

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A1, A2, a1, a2
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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O1, o2
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A1, A2, a1, a2
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNL
Query on UNL

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A1, A2, B1, B2, C2, D1, F2, H2, I2, J2, K2, M2, W2, X2, a1, a2, b1, b2, c2, d1, d2, i2, j1, k2, l1, m1, m2, t1, x1
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.445α = 90
b = 240.31β = 90
c = 300.063γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHARPphasing
SOLVEphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-03-19 
  • Released Date: 2016-01-20 
  • Deposition Author(s): Ago, H., Shen, J.-R.

Funding OrganizationLocationGrant Number
JSPSJapan24000018

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 1.2: 2016-03-23
    Changes: Database references
  • Version 1.3: 2020-02-05
    Changes: Data collection, Database references, Derived calculations