5H2F

Crystal structure of the PsbM-deletion mutant of photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II.

Uto, S.Kawakami, K.Umena, Y.Iwai, M.Ikeuchi, M.Shen, J.R.Kamiya, N.

(2017) Faraday Discuss. 198: 107-120

  • DOI: 10.1039/c6fd00213g

  • PubMed Abstract: 
  • Photosystem II (PSII) is a membrane protein complex that performs light-induced electron transfer and oxygen evolution from water. PSII consists of 19 or 20 subunits in its crystal form and binds various cofactors such as chlorophyll a, plastoquinone ...

    Photosystem II (PSII) is a membrane protein complex that performs light-induced electron transfer and oxygen evolution from water. PSII consists of 19 or 20 subunits in its crystal form and binds various cofactors such as chlorophyll a, plastoquinone, carotenoid, and lipids. After initial light excitation, the charge separation produces an electron, which is transferred to a plastoquinone molecule (QA) and then to another plastoquinone (QB). PsbM is a low-molecular-weight subunit with one transmembrane helix, and is located in the monomer-monomer interface of the PSII dimer. The function of PsbM has been reported to be stabilization of the PSII dimer and maintenance of electron transfer efficiency of PSII based on previous X-ray crystal structure analysis at a resolution of 4.2 Å. In order to elucidate the structure-function relationships of PsbM in detail, we improved the quality of PSII crystals from a PsbM-deleted mutant (ΔPsbM-PSII) of Thermosynechococcus elongatus, and succeeded in improving the diffraction quality to a resolution of 2.2 Å. X-ray crystal structure analysis of ΔPsbM-PSII showed that electron densities for the PsbM subunit and neighboring carotenoid and detergent molecules were absent in the monomer-monomer interface. The overall structure of ΔPsbM-PSII was similar to wild-type PSII, but the arrangement of the hydrophobic transmembrane subunits was significantly changed by the deletion of PsbM, resulting in a slight widening of the lipid hole involving QB. The lipid hole-widening further induced structural changes of the bicarbonate ion coordinated to the non-heme Fe(ii) atom and destabilized the polypeptide chains around the QB binding site located far from the position of PsbM. The fluorescence decay measurement indicated that the electron transfer rate from QA to QB was decreased in ΔPsbM-PSII compared with wild-type PSII. The functional change in electron transfer efficiency was fully interpreted based on structural changes caused by the deletion of the PsbM subunit.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, Japan. nkamiya@sci.osaka-cu.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein D1 1
A, a
334Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbA1 (psbA-1)
EC: 1.10.3.9
Find proteins for P0A444 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A444
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center protein
B, b
505Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbB
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 reaction center protein
C, c
455Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbC
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIF8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D, d
342Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbD1, psbD2
EC: 1.10.3.9
Find proteins for Q8CM25 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8CM25
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
80Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbE
Find proteins for Q8DIP0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIP0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
33Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbF
Find proteins for Q8DIN9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
63Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbH
Find proteins for Q8DJ43 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJ43
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
36Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbI
Find proteins for Q8DJZ6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJZ6
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
40Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbJ
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P59087
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
37Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbK
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1K9
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
35Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbL
Find proteins for Q8DIN8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
243Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbO
Find proteins for P0A431 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A431
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
30Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbT
Find proteins for Q8DIQ0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ0
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
97Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbU
Find proteins for Q9F1L5 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1L5
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbV
Find proteins for P0A386 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A386
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y, y
29Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ycf12
Find proteins for Q8DJI1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJI1
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center X protein
X, x
37Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbX
Find proteins for Q9F1R6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1R6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: psbZ
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DHJ2
Small Molecules
Ligands 19 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

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A, a, b, C, D, f, 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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A, a, b, B, c, C, d, D
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

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a, A, 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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A, a
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, a
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HTG
Query on HTG

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B, b, c, C, D, l, v, V
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
CA
Query on CA

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b, B, c, O, o
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DGD
Query on DGD

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

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A, B, b, c, C, d, D, i, J, j
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
MG
Query on MG

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j, J, k, K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 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, d, D, K, k, y, Y
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

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A, a, 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
LMT
Query on LMT

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A, a, B, c, E, f, I, t, T, Z
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
DMS
Query on DMS

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a, A, B, b, c, C, D, d, F, f, H, i, I, L, l, o, O, t, U, u, V, v
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
RRX
Query on RRX

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h, H
(3R)-beta,beta-caroten-3-ol
beta-Cryptoxanthin
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
 Ligand Interaction
LHG
Query on LHG

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A, a, C, d, D, L, l
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
i, I, T, t
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 121.954α = 90.00
b = 226.993β = 90.00
c = 285.886γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata reduction
MOLREPphasing
REFMACrefinement
MOLREPphasing
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHI GrantsJapan24227002
Grant-in-Aid for Scientific Research on Innovative Areas Artificial photosynthesis (AnApple)Japan24107003

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Data collection, Database references