5ZZN

Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.

Nakajima, Y., Umena, Y., Nagao, R., Endo, K., Kobayashi, K., Akita, F., Suga, M., Wada, H., Noguchi, T., Shen, J.R.

(2018) J Biol Chem 293: 14786-14797

  • DOI: 10.1074/jbc.RA118.004304
  • Primary Citation of Related Structures:  
    5ZZN

  • PubMed Abstract: 

    • Sulfoquinovosyl-diacylglycerol (SQDG) is one of the four lipids present in the thylakoid membranes. Depletion of SQDG causes different degrees of effects on photosynthetic growth and activities in different organisms. Four SQDG molecules bind to each monomer of photosystem II (PSII), but their role in PSII function has not been characterized in detail, and no PSII structure without SQDG has been reported ...

    Sulfoquinovosyl-diacylglycerol (SQDG) is one of the four lipids present in the thylakoid membranes. Depletion of SQDG causes different degrees of effects on photosynthetic growth and activities in different organisms. Four SQDG molecules bind to each monomer of photosystem II (PSII), but their role in PSII function has not been characterized in detail, and no PSII structure without SQDG has been reported. We analyzed the activities of PSII from an SQDG-deficient mutant of the cyanobacterium Thermosynechococcus elongatus by various spectroscopic methods, which showed that depletion of SQDG partially impaired the PSII activity by impairing secondary quinone (Q B ) exchange at the acceptor site. We further solved the crystal structure of the PSII dimer from the SQDG deletion mutant at 2.1 Å resolution and found that all of the four SQDG-binding sites were occupied by other lipids, most likely PG molecules. Replacement of SQDG at a site near the head of Q B provides a possible explanation for the Q B impairment. The replacement of two SQDGs located at the monomer-monomer interface by other lipids decreased the stability of the PSII dimer, resulting in an increase in the amount of PSII monomer in the mutant. The present results thus suggest that although SQDG binding in all of the PSII-binding sites is necessary to fully maintain the activity and stability of PSII, replacement of SQDG by other lipids can partially compensate for their functions.

    Organizational Affiliation: 

    From the Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, shen@cc.okayama-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein D1 1 A, a334Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbA1, psbA-1, tlr1843
EC: 1.10.3.9
Find proteins for P0A444 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center protein B, b505Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbB, tlr1530
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center protein C, c455Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbC, tlr1631
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 protein D, d342Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbD1, tlr0455, psbD2, tlr1630
EC: 1.10.3.9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alpha E, e81Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbE, tsr1541
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Entity ID: 6
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Cytochrome b559 subunit beta F, f34Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbF, tsr1542
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein H H, h63Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbH, tsl1386
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Entity ID: 8
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Photosystem II reaction center protein I I, i37Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbI, tsr1074
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Entity ID: 9
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Photosystem II reaction center protein J J, j40Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbJ, tsr1544
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 10
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Photosystem II reaction center protein K K, k37Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbK, tsl0176
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 11
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Photosystem II reaction center protein L L, l36Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbL, tsr1543
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Entity ID: 12
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Photosystem II reaction center protein M M, m34Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbM, tsl2052
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Entity ID: 13
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Photosystem II manganese-stabilizing polypeptide O, o243Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbO, tll0444
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein T T, t30Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbT, tsr1531
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Entity ID: 15
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Photosystem II 12 kDa extrinsic protein U, u97Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbU, tll2409
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Entity ID: 16
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Cytochrome c-550 V, v137Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbV, tll1285
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Entity ID: 17
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Photosystem II reaction center protein Ycf12 Y, y29Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: ycf12, tsr1242
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Entity ID: 18
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Photosystem II reaction center X protein X, x39Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbX, tsr2013
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Entity ID: 19
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Photosystem II reaction center protein Z Z, z62Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbZ, tsr1967
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1))
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  • Reference Sequence
Small Molecules
Ligands 21 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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C, D, H, c, d, h
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N		 Ligand Interaction
CLA
Query on CLA
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A, B, C, D, a, b, c, d
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M		 Ligand Interaction
PHO
Query on PHO
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A, D, a, d
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N		 Ligand Interaction
LMG
Query on LMG
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A, B, C, D, a, b, c, d
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N		 Ligand Interaction
PL9
Query on PL9
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A, D, a, 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		 Ligand Interaction
LHG
Query on LHG
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B, D, E, F, b, d, e, f
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N		 Ligand Interaction
HEC
Query on HEC
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V, v
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
HEM
Query on HEM
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F, f
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
RRX
Query on RRX
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H, h
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N		 Ligand Interaction
BCR
Query on BCR
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A, B, C, D, K, T, Y, a, b, c, d, k, t, y
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N		 Ligand Interaction
LMT
Query on LMT
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A, B, C, F, J, M, T, Z, a, b, c, j, l, m, t, z
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N		 Ligand Interaction
UNL
Query on UNL
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A, B, C, D, E, H, I, J, K, T, U, X, Z, a, b, c, d, e, h, i, j, t, u, x
cyclohexylmethyl-[[2-[[(4-oxidanylidenepyrido[1,2-a]pyrimidin-2-yl)carbonylamino]methyl]imidazo[1,2-a]pyridin-6-yl]methyl]azanium
C25 H29 N6 O2
OBERVORNENYOLE-UHFFFAOYSA-O		 Ligand Interaction
OEX
Query on OEX
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A, a
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N		 Ligand Interaction
HTG
Query on HTG
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B, C, D, O, U, V, b, c, d, o, v
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N		 Ligand Interaction
GOL
Query on GOL
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C, D, b, c, e
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
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A, B, C, D, E, I, O, U, V, a, b, c, d, e, h, o, u, v
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
BCT
Query on BCT
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D, d
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M		 Ligand Interaction
FE2
Query on FE2
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D, a
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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B, O, V, b, c, o, v
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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A, a, v
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
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J, K, j, k
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
HSK
Query on HSK		D,dL-PEPTIDE LINKINGC6 H9 N3 O3HIS
FME
Query on FME		I,iL-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.25α = 90
b = 228.43β = 90
c = 287.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP17H06434
Japan Society for the Promotion of ScienceJapanJP16K21181
Japan Science and TechnologyJapanJPMJPR16P1

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references
  • Version 2.0: 2019-10-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary