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 

Starting Model: experimental
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This is version 3.0 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: https://doi.org/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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
T [auth a]
334Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]
505Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]
455Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]
342Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]
81Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]
63Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]
40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]
36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]
243Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]
30Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]
97Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]
137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
Q [auth Y]
29Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinKA [auth x],
R [auth X]
39Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 21 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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DM [auth h]
GK [auth c]
HK [auth c]
IK [auth c]
JF [auth H]
DM [auth h],
GK [auth c],
HK [auth c],
IK [auth c],
JF [auth H],
MD [auth C],
ML [auth d],
ND [auth C],
OD [auth C],
PE [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AD [auth C]
AK [auth c]
BD [auth C]
BK [auth c]
CD [auth C]
AD [auth C],
AK [auth c],
BD [auth C],
BK [auth c],
CD [auth C],
CK [auth c],
DD [auth C],
DK [auth c],
ED [auth C],
FD [auth C],
FI [auth b],
GD [auth C],
GI [auth b],
GL [auth d],
HD [auth C],
HI [auth b],
HL [auth d],
IB [auth B],
ID [auth C],
II [auth b],
JB [auth B],
JD [auth C],
JI [auth b],
JL [auth d],
KB [auth B],
KD [auth C],
KE [auth D],
KI [auth b],
LB [auth B],
LH [auth a],
LI [auth b],
MB [auth B],
ME [auth D],
MH [auth a],
MI [auth b],
NB [auth B],
NI [auth b],
OB [auth B],
OH [auth a],
OI [auth b],
PA [auth A],
PB [auth B],
PI [auth b],
QA [auth A],
QB [auth B],
QI [auth b],
RA [auth A],
RB [auth B],
RI [auth b],
RJ [auth c],
SB [auth B],
SI [auth b],
SJ [auth c],
TA [auth A],
TB [auth B],
TI [auth b],
TJ [auth c],
UB [auth B],
UI [auth b],
UJ [auth c],
VB [auth B],
VJ [auth c],
WB [auth B],
WJ [auth c],
XB [auth B],
XJ [auth c],
YC [auth C],
YJ [auth c],
ZC [auth C],
ZJ [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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IL [auth d],
LE [auth D],
NH [auth a],
SA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
LMG
Query on LMG

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CC [auth B]
JK [auth c]
KK [auth c]
PD [auth C]
QD [auth C]
CC [auth B],
JK [auth c],
KK [auth c],
PD [auth C],
QD [auth C],
QL [auth d],
RH [auth a],
TE [auth D],
WA [auth A],
ZI [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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LL [auth d],
OE [auth D],
QH [auth a],
VA [auth A]
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
LHG
Query on LHG

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BC [auth B]
CF [auth E]
CM [auth f]
IF [auth F]
NL [auth d]
BC [auth B],
CF [auth E],
CM [auth f],
IF [auth F],
NL [auth d],
OL [auth d],
PL [auth d],
QE [auth D],
RE [auth D],
SE [auth D],
WL [auth e],
YI [auth b]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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ON [auth v],
TG [auth V]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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BM [auth f],
GF [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX
Query on RRX

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EM [auth h],
KF [auth H]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR

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AC [auth B]
CH [auth Y]
EK [auth c]
FK [auth c]
GN [auth t]
AC [auth B],
CH [auth Y],
EK [auth c],
FK [auth c],
GN [auth t],
KL [auth d],
LD [auth C],
NE [auth D],
NG [auth T],
PH [auth a],
PM [auth k],
UA [auth A],
VF [auth K],
VI [auth b],
WF [auth K],
WI [auth b],
WN [auth y],
XI [auth b],
YB [auth B],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AB [auth A]
AG [auth M]
AJ [auth b]
DC [auth B]
EH [auth Z]
AB [auth A],
AG [auth M],
AJ [auth b],
DC [auth B],
EH [auth Z],
GH [auth a],
HF [auth F],
HN [auth t],
LK [auth c],
MM [auth j],
OG [auth T],
RD [auth C],
RM [auth l],
SM [auth m],
TF [auth J],
TM [auth m],
UM [auth m],
YN [auth z],
ZF [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

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HH [auth a],
MA [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG

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BI [auth b]
BJ [auth b]
CG [auth O]
CI [auth b]
EC [auth B]
BI [auth b],
BJ [auth b],
CG [auth O],
CI [auth b],
EC [auth B],
EL [auth c],
GE [auth C],
HE [auth C],
IC [auth B],
JC [auth B],
MK [auth c],
NK [auth c],
OJ [auth b],
RL [auth d],
SD [auth C],
SG [auth U],
TD [auth C],
UE [auth D],
UG [auth V],
UN [auth v],
VM [auth o],
WC [auth B]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL

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EE [auth C],
KJ [auth b],
WK [auth c],
YE [auth D],
ZL [auth e]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

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AE [auth C]
AF [auth D]
AH [auth V]
AL [auth c]
AM [auth e]
AE [auth C],
AF [auth D],
AH [auth V],
AL [auth c],
AM [auth e],
AN [auth o],
BB [auth A],
BE [auth C],
BF [auth D],
BL [auth c],
BN [auth o],
CB [auth A],
CE [auth C],
CL [auth c],
CN [auth o],
DB [auth A],
DE [auth C],
DG [auth O],
DL [auth c],
DN [auth o],
EB [auth A],
EG [auth O],
EJ [auth b],
EN [auth o],
FE [auth C],
FF [auth E],
FG [auth O],
FJ [auth b],
FN [auth o],
GG [auth O],
GJ [auth b],
GM [auth h],
HG [auth O],
HJ [auth b],
IG [auth O],
IJ [auth b],
JG [auth O],
JJ [auth b],
KG [auth O],
KN [auth u],
LC [auth B],
LG [auth O],
LJ [auth b],
LN [auth u],
MC [auth B],
MG [auth O],
MJ [auth b],
MN [auth u],
NC [auth B],
NJ [auth b],
OC [auth B],
PC [auth B],
PN [auth v],
QC [auth B],
QN [auth v],
RC [auth B],
RF [auth I],
RG [auth U],
RK [auth c],
RN [auth v],
SC [auth B],
SK [auth c],
SN [auth v],
TC [auth B],
TK [auth c],
TL [auth d],
TN [auth v],
UC [auth B],
UK [auth c],
UL [auth d],
VC [auth B],
VG [auth V],
VH [auth a],
VK [auth c],
WD [auth C],
WE [auth D],
WG [auth V],
WH [auth a],
XD [auth C],
XE [auth D],
XG [auth V],
XH [auth a],
XK [auth c],
XM [auth o],
YD [auth C],
YG [auth V],
YH [auth a],
YK [auth c],
YM [auth o],
ZD [auth C],
ZE [auth D],
ZG [auth V],
ZH [auth a],
ZK [auth c],
ZM [auth o]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT
Query on BCT

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FL [auth d],
JE [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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IE [auth D],
IH [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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BG [auth O]
BH [auth V]
EI [auth b]
HB [auth B]
QJ [auth c]
BG [auth O],
BH [auth V],
EI [auth b],
HB [auth B],
QJ [auth c],
VN [auth v],
WM [auth o]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
JH [auth a],
KH [auth a],
NA [auth A],
NN [auth v],
OA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
LM [auth j],
QM [auth k],
SF [auth J],
YF [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL

Download Ideal Coordinates CCD File 
AI [auth a]
CJ [auth b]
DF [auth E]
DH [auth X]
DI [auth b]
AI [auth a],
CJ [auth b],
DF [auth E],
DH [auth X],
DI [auth b],
DJ [auth b],
EF [auth E],
FB [auth A],
FC [auth B],
FH [auth Z],
FM [auth h],
GB [auth A],
GC [auth B],
HC [auth B],
HM [auth i],
IM [auth i],
IN [auth t],
JM [auth i],
JN [auth u],
KC [auth B],
KM [auth i],
LF [auth H],
MF [auth H],
NF [auth I],
NM [auth j],
OF [auth I],
OK [auth c],
OM [auth j],
PF [auth I],
PG [auth T],
PJ [auth b],
PK [auth c],
QF [auth I],
QG [auth U],
QK [auth c],
SH [auth a],
SL [auth d],
TH [auth a],
UD [auth C],
UF [auth J],
UH [auth a],
VD [auth C],
VE [auth D],
VL [auth d],
XA [auth A],
XC [auth B],
XF [auth K],
XL [auth e],
XN [auth x],
YA [auth A],
YL [auth e],
ZA [auth A]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HSK
Query on HSK
D,
W [auth d]
L-PEPTIDE LINKINGC6 H9 N3 O3HIS
FME
Query on FME
AA [auth i],
H [auth I]
L-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

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 3.0: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary