4PJ0

Structure of T.elongatus Photosystem II, rows of dimers crystal packing

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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This is version 3.0 of the entry. See complete history. 


Literature

Native-like Photosystem II Superstructure at 2.44 angstrom Resolution through Detergent Extraction from the Protein Crystal.

Hellmich, J., Bommer, M., Burkhardt, A., Ibrahim, M., Kern, J., Meents, A., Muh, F., Dobbek, H., Zouni, A.

(2014) Structure 22: 1607-1615

  • DOI: https://doi.org/10.1016/j.str.2014.09.007
  • Primary Citation of Related Structures:  
    4PJ0

  • PubMed Abstract: 

    Photosystem II (PSII) catalyzes a key step in photosynthesis, the oxidation of water to oxygen. Excellent structural models exist for the dimeric PSII core complex of cyanobacteria, but higher order physiological assemblies readily dissociate when solubilized from the native thylakoid membrane with detergent. Here, we describe the crystallization of PSII from Thermosynechococcus elongatus with a postcrystallization treatment involving extraction of the detergent C12E8. This resulted in a transition from Type II to Type I-like membrane protein crystals and improved diffraction to 2.44 Å resolution. The obtained PSII packing in precise rows, interconnected by specific pairs of galactolipids and a loop in the PsbO subunit specific to cyanobacteria, is superimposable with previous electron microscopy images of the thylakoid membrane. The study provides a detailed model of such a superstructure and its organization of light-harvesting pigments with possible implications for the understanding of their efficient use of solar energy.

    • Organizational Affiliation: 

    Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10095 Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A,
T [auth a]		344Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CP47 proteinB,
U [auth b]		510Thermosynechococcus vestitusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC,
V [auth c]		461Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]		352Thermosynechococcus 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]		84Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]		45Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
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]		66Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
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]		38Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
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 
EC: 1.10.3.9
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]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]		37Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
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]		36Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]		272Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
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]		32Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
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]		134Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]		163Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12MA [auth y],
Q [auth Y]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinJA [auth x],
R [auth X]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZNA [auth z],
S [auth Z]		62Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YKA [auth R],
LA [auth r]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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HH [auth h]
NG [auth c]
OG [auth c]
PD [auth H]
PG [auth c]
HH [auth h],
NG [auth c],
OG [auth c],
PD [auth H],
PG [auth c],
UC [auth C],
VC [auth C],
WC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA
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AF [auth b]
AG [auth c]
BF [auth b]
BG [auth c]
CF [auth b]
AF [auth b],
AG [auth c],
BF [auth b],
BG [auth c],
CF [auth b],
CG [auth c],
DD [auth D],
DF [auth b],
DG [auth c],
EB [auth B],
ED [auth D],
EF [auth b],
EG [auth c],
FB [auth B],
FC [auth C],
FD [auth D],
FF [auth b],
FG [auth c],
GB [auth B],
GC [auth C],
GF [auth b],
GG [auth c],
HB [auth B],
HC [auth C],
HF [auth b],
HG [auth c],
IB [auth B],
IC [auth C],
IF [auth b],
IG [auth c],
JB [auth B],
JC [auth C],
JF [auth b],
JG [auth c],
KB [auth B],
KC [auth C],
KF [auth b],
KG [auth c],
LB [auth B],
LC [auth C],
LF [auth b],
LG [auth c],
MB [auth B],
MC [auth C],
ME [auth a],
MF [auth b],
NB [auth B],
NC [auth C],
NE [auth a],
NF [auth b],
OB [auth B],
OC [auth C],
OE [auth a],
OF [auth b],
PB [auth B],
PC [auth C],
QB [auth B],
QC [auth C],
QE [auth a],
RB [auth B],
RC [auth C],
SB [auth B],
TA [auth A],
TB [auth B],
UA [auth A],
UG [auth d],
VA [auth A],
WG [auth d],
ZE [auth b],
ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO
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BD [auth D],
CD [auth D],
PE [auth a],
VG [auth d]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD
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FH [auth f]
ND [auth F]
TD [auth L]
TE [auth a]
VD [auth L]
FH [auth f],
ND [auth F],
TD [auth L],
TE [auth a],
VD [auth L],
YA [auth A]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG
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BC [auth B]
BH [auth d]
JD [auth D]
JE [auth a]
QA [auth A]
BC [auth B],
BH [auth d],
JD [auth D],
JE [auth a],
QA [auth A],
QG [auth c],
SF [auth b],
SG [auth c],
UE [auth a],
WF [auth b],
XB [auth B],
XC [auth C],
ZA [auth A],
ZC [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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HD [auth D],
SE [auth a],
XA [auth A],
YG [auth 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
LHG
Query on LHG
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AB [auth A]
AH [auth d]
BB [auth A]
ID [auth D]
LD [auth E]
AB [auth A],
AH [auth d],
BB [auth A],
ID [auth D],
LD [auth E],
MH [auth l],
UD [auth L],
VE [auth a],
WE [auth a],
ZG [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC
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EE [auth V],
UH [auth v]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM
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EH [auth e],
MD [auth E]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR
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AD [auth C]
AE [auth T]
GD [auth D]
GH [auth h]
LH [auth k]
AD [auth C],
AE [auth T],
GD [auth D],
GH [auth h],
LH [auth k],
MG [auth c],
OD [auth H],
PF [auth b],
QF [auth b],
RE [auth a],
RF [auth b],
RH [auth t],
SC [auth C],
SD [auth K],
TC [auth C],
TG [auth c],
UB [auth B],
VB [auth B],
WA [auth A],
WB [auth B],
WH [auth z],
XG [auth d]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX
Query on OEX
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HE [auth a],
OA [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
SO4
Query on SO4
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CB [auth A]
DE [auth U]
DH [auth d]
FE [auth V]
PH [auth o]
CB [auth A],
DE [auth U],
DH [auth d],
FE [auth V],
PH [auth o],
SH [auth u],
TH [auth u],
XE [auth a],
YD [auth O],
ZD [auth O]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BCT
Query on BCT
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DB [auth A],
YE [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE
Query on FE
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IE [auth a],
PA [auth A]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL
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KE [auth a],
LE [auth a],
RA [auth A],
SA [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL
Query on UNL
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AC [auth B]
BE [auth T]
CC [auth B]
CE [auth T]
CH [auth d]
AC [auth B],
BE [auth T],
CC [auth B],
CE [auth T],
CH [auth d],
DC [auth B],
EC [auth B],
GE [auth X],
IH [auth i],
JH [auth j],
KD [auth D],
KH [auth k],
NH [auth m],
OH [auth m],
QD [auth I],
QH [auth t],
RD [auth J],
RG [auth c],
TF [auth b],
UF [auth b],
VF [auth b],
VH [auth x],
WD [auth M],
XD [auth M],
XF [auth b],
YB [auth B],
YC [auth C],
YF [auth b],
ZB [auth B]
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.447α = 90
b = 218.889β = 90
c = 302.202γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Structure summary
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 2.0: 2021-03-10
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary
  • Version 3.0: 2023-09-27
    Changes: Data collection, Database references, Non-polymer description, Refinement description