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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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

    From the RIKEN SPring-8 Center, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein D1
A1, a1, A2, a2
344Cyanidium caldariumGene Names: psbA
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19895 (Cyanidium caldarium)
Go to UniProtKB:  O19895
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center protein
B1, b1, B2, b2
509Cyanidium caldariumGene Names: psbB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19928 (Cyanidium caldarium)
Go to UniProtKB:  O19928
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 reaction center protein
C1, c1, C2, c2
460Cyanidium caldariumGene Names: psbC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM46 (Cyanidium caldarium)
Go to UniProtKB:  Q9TM46
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D1, d1, D2, d2
351Cyanidium caldariumGene Names: psbD
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM47 (Cyanidium caldarium)
Go to UniProtKB:  Q9TM47
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E1, e1, E2, e2
84Cyanidium caldariumGene Names: psbE
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM20 (Cyanidium caldarium)
Go to UniProtKB:  Q9TM20
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F1, f1, F2, f2
43Cyanidium caldariumGene Names: psbF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM21 (Cyanidium caldarium)
Go to UniProtKB:  Q9TM21
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H1, h1, H2, h2
67Cyanidium caldariumGene Names: psbH
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19925 (Cyanidium caldarium)
Go to UniProtKB:  O19925
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I1, i1, I2, i2
38Cyanidium caldariumGene Names: psbI
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19882 (Cyanidium caldarium)
Go to UniProtKB:  O19882
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J1, j1, J2, j2
39Cyanidium caldariumGene Names: psbJ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM23 (Cyanidium caldarium)
Go to UniProtKB:  Q9TM23
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K1, k1, K2, k2
41Cyanidium caldariumGene Names: psbK
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TLR0 (Cyanidium caldarium)
Go to UniProtKB:  Q9TLR0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L1, l1, L2, l2
38Cyanidium caldariumGene Names: psbL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TM22 (Cyanidium caldarium)
Go to UniProtKB:  Q9TM22
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM II REACTION CENTER PROTEIN M
M1, m1, M2, m2
108N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
O1, o1, O2, o2
329N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T1, t1, T2, t2
32Cyanidium caldariumGene Names: psbT
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for O19927 (Cyanidium caldarium)
Go to UniProtKB:  O19927
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein, chloroplastic
U1, u1, U2, u2
155Cyanidium caldariumGene Names: psbU
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9ZQS5 (Cyanidium caldarium)
Go to UniProtKB:  Q9ZQS5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V1, v1, V2, v2
155Cyanidium caldariumGene Names: psbV
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q76FB0 (Cyanidium caldarium)
Go to UniProtKB:  Q76FB0
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y1, y1, Y2, y2
35Cyanidium caldariumGene Names: ycf12 (ycf34)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q9TLX0 (Cyanidium caldarium)
Go to UniProtKB:  Q9TLX0
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYSTEM II REACTION CENTER PROTEIN X
X1, x1, X2, x2
40N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE CHAIN UNASSIGNED
S1, s1, S2, s2
46N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE CHAIN UNASSIGNED
W1, w1, W2, w2
25N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Extrinsic protein in photosystem II
q1, Q2
218Cyanidium caldariumGene Names: psbQ'
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II from a red alga
Find proteins for Q76B86 (Cyanidium caldarium)
Go to UniProtKB:  Q76B86
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z2, z2
62N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 16 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

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b2, B2, D1, D2
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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a1, A1, a2, A2, b1, B1, b2, B2, c1, C1, c2, C2, D1, d1, d2, D2, K2
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

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D1, d1, D2, 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
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
OEX
Query on OEX

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

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

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a1, a2, B1, b1, c1, C1, c2, C2, i1
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

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

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

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Download CCD File 
a1, A1, a2, A2
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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

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

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

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

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

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Download CCD File 
a1, a2, A2, B1, b1, B2, b2, d1, D1, D2, d2, l1, L1, l2, L2
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 210.445α = 90.00
b = 240.310β = 90.00
c = 300.063γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 OrganizationCountryGrant Number
JSPSJapan24000018

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-02-03
    Type: Database references
  • Version 1.2: 2016-03-23
    Type: Database references