7RCV

High-resolution structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803.

Gisriel, C.J., Wang, J., Liu, J., Flesher, D.A., Reiss, K.M., Huang, H.L., Yang, K.R., Armstrong, W.H., Gunner, M.R., Batista, V.S., Debus, R.J., Brudvig, G.W.

(2022) Proc Natl Acad Sci U S A 119

  • DOI: https://doi.org/10.1073/pnas.2116765118
  • Primary Citation of Related Structures:  
    7N8O, 7RCV

  • PubMed Abstract: 

    Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.

    • Organizational Affiliation: 

    Department of Chemistry, Yale University, New Haven, CT 06520.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1 2A,
V [auth a]		360Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P16033 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
W [auth b]		507Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
X [auth c]		460Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
Y [auth d]		352Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Z [auth e]		81Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaAA [auth f],
F		44Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HBA [auth h],
G [auth H]		64Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ICA [auth i],
H [auth I]		38Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JDA [auth j],
I [auth J]		39Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KEA [auth k],
J [auth K]		45Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LFA [auth l],
K [auth L]		39Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MGA [auth m],
L [auth M]		35Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideHA [auth o],
M [auth O]		247Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Sll1638 proteinIA [auth q],
N [auth Q]		149Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YJA [auth r],
O [auth R]		39Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TKA [auth t],
P [auth T]		31Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinLA [auth u],
Q [auth U]		131Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550MA [auth v],
R [auth V]		160Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinNA [auth x],
S [auth X]		39Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12OA [auth y],
T [auth Y]		39Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZPA [auth z],
U [auth Z]		62Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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BE [auth H]
HH [auth c]
IH [auth c]
JH [auth c]
LI [auth h]
BE [auth H],
HH [auth c],
IH [auth c],
JH [auth c],
LI [auth h],
XC [auth C],
YC [auth C],
ZC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA
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AG [auth b]
AH [auth c]
BG [auth b]
BH [auth c]
CG [auth b]
AG [auth b],
AH [auth c],
BG [auth b],
BH [auth c],
CG [auth b],
CH [auth c],
DG [auth b],
DH [auth c],
EG [auth b],
EH [auth c],
FF [auth a],
FG [auth b],
FH [auth c],
GF [auth a],
GG [auth b],
HD [auth D],
HG [auth b],
IF [auth a],
IG [auth b],
JB [auth B],
JC [auth C],
JD [auth D],
JG [auth b],
KB [auth B],
KC [auth C],
KD [auth D],
LB [auth B],
LC [auth C],
MB [auth B],
MC [auth C],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
PB [auth B],
PC [auth C],
QB [auth B],
QC [auth C],
RB [auth B],
RC [auth C],
RH [auth d],
SB [auth B],
SC [auth C],
TB [auth B],
TC [auth C],
TG [auth c],
TH [auth d],
UA [auth A],
UB [auth B],
UC [auth C],
UF [auth b],
UG [auth c],
UH [auth d],
VA [auth A],
VB [auth B],
VC [auth C],
VF [auth b],
VG [auth c],
WB [auth B],
WF [auth b],
WG [auth c],
XA [auth A],
XB [auth B],
XF [auth b],
XG [auth c],
YB [auth B],
YF [auth b],
YG [auth c],
ZF [auth b],
ZG [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO
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HF [auth a],
ID [auth D],
SH [auth d],
WA [auth A]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
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AE [auth H]
CB [auth A]
CC [auth B]
DB [auth A]
GI [auth f]
AE [auth H],
CB [auth A],
CC [auth B],
DB [auth A],
GI [auth f],
HE [auth K],
KF [auth a],
KI [auth h],
NF [auth a],
OF [auth a],
PE [auth T],
RI [auth k],
WD [auth F],
ZA [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
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AB [auth A]
AD [auth C]
DC [auth B]
EB [auth A]
FD [auth C]
AB [auth A],
AD [auth C],
DC [auth B],
EB [auth A],
FD [auth C],
KH [auth c],
LF [auth a],
NG [auth b],
PD [auth D],
PF [auth a],
PH [auth c],
ZH [auth d]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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BB [auth A],
MD [auth D],
MF [auth a],
WH [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
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AF [auth Z]
EC [auth B]
EI [auth e]
IB [auth A]
JJ [auth z]
AF [auth Z],
EC [auth B],
EI [auth e],
IB [auth A],
JJ [auth z],
LE [auth L],
ND [auth D],
OD [auth D],
OG [auth b],
TF [auth a],
UD [auth E],
VI [auth l],
XH [auth d],
YH [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
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BJ [auth v],
HI [auth f],
SE [auth V],
XD [auth F]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX
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EJ [auth x],
VE [auth X]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
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AC [auth B]
BC [auth B]
ED [auth C]
GH [auth c]
IE [auth K]
AC [auth B],
BC [auth B],
ED [auth C],
GH [auth c],
IE [auth K],
IJ [auth z],
JF [auth a],
KG [auth b],
LD [auth D],
LG [auth b],
MG [auth b],
OH [auth c],
SI [auth k],
VH [auth d],
WC [auth C],
YA [auth A],
ZB [auth B],
ZE [auth Z]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
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AI [auth d]
BD [auth C]
BI [auth d]
CD [auth C]
CE [auth I]
AI [auth d],
BD [auth C],
BI [auth d],
CD [auth C],
CE [auth I],
CI [auth d],
DD [auth C],
DE [auth I],
DI [auth e],
DJ [auth x],
EE [auth I],
FB [auth A],
FC [auth B],
FE [auth I],
FI [auth e],
FJ [auth x],
GB [auth A],
GC [auth B],
GD [auth C],
GE [auth J],
GJ [auth x],
HC [auth B],
HJ [auth y],
IC [auth B],
II [auth f],
JI [auth h],
KE [auth K],
LH [auth c],
ME [auth M],
MH [auth c],
MI [auth i],
NE [auth M],
NH [auth c],
NI [auth i],
OE [auth M],
OI [auth i],
PG [auth b],
PI [auth i],
QD [auth D],
QE [auth T],
QF [auth a],
QG [auth b],
QH [auth c],
QI [auth j],
RD [auth D],
RF [auth a],
RG [auth b],
SD [auth D],
SG [auth b],
TD [auth E],
UE [auth X],
UI [auth k],
VD [auth E],
WE [auth X],
WI [auth m],
XE [auth X],
XI [auth m],
YD [auth F],
YE [auth Y],
YI [auth m],
ZD [auth H],
ZI [auth t]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX (Subject of Investigation/LOI)
Query on OEX
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BF [auth a],
QA [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT
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HB [auth A],
SF [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
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CF [auth a],
RA [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA
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AJ [auth u]
CJ [auth v]
JE [auth K]
RE [auth U]
TE [auth V]
AJ [auth u],
CJ [auth v],
JE [auth K],
RE [auth U],
TE [auth V],
TI [auth k]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
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DF [auth a],
EF [auth a],
SA [auth A],
TA [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME		CA [auth i],
H [auth I]		L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-FG02-05ER15646

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2022-01-05
    Changes: Database references