9EVX

cryoEM structure of Photosystem II averaged across S2-S3 states at 1.71 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II.

Hussein, R.Graca, A.Forsman, J.Aydin, A.O.Hall, M.Gaetcke, J.Chernev, P.Wendler, P.Dobbek, H.Messinger, J.Zouni, A.Schroder, W.P.

(2024) Science 384: 1349-1355

  • DOI: https://doi.org/10.1126/science.adn6541
  • Primary Citation of Related Structures:  
    9EVX

  • PubMed Abstract: 

    Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo-electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.


  • Organizational Affiliation

    Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
T [auth a]
344Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]
510Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]
461Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]
84Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]
45Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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): 1 
UniProt
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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 
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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 
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 
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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 
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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 
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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 
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 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]
163Thermosynechococcus vestitus BP-1Mutation(s): 0 
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 X proteinJA [auth x],
Q [auth X]
41Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth y],
R [auth Y]
46Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AF [auth a]
AH [auth c]
BI [auth h]
WC [auth C]
XC [auth C]
AF [auth a],
AH [auth c],
BI [auth h],
WC [auth C],
XC [auth C],
YA [auth A],
YC [auth C],
YG [auth c],
ZD [auth H],
ZG [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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EB [auth A]
GC [auth C]
GF [auth a]
HB [auth B]
HC [auth C]
EB [auth A],
GC [auth C],
GF [auth a],
HB [auth B],
HC [auth C],
IB [auth B],
IC [auth C],
ID [auth D],
IG [auth c],
JB [auth B],
JC [auth C],
JD [auth D],
JG [auth c],
KB [auth B],
KC [auth C],
KF [auth b],
KG [auth c],
KH [auth d],
LB [auth B],
LC [auth C],
LF [auth b],
LG [auth c],
LH [auth d],
MB [auth B],
MC [auth C],
MF [auth b],
MG [auth c],
NB [auth B],
NC [auth C],
NF [auth b],
NG [auth c],
OB [auth B],
OC [auth C],
OF [auth b],
OG [auth c],
PA [auth A],
PB [auth B],
PC [auth C],
PF [auth b],
PG [auth c],
QA [auth A],
QB [auth B],
QC [auth C],
QF [auth b],
QG [auth c],
RA [auth A],
RB [auth B],
RC [auth C],
RE [auth a],
RF [auth b],
RG [auth c],
SB [auth B],
SC [auth C],
SE [auth a],
SF [auth b],
SG [auth c],
TB [auth B],
TE [auth a],
TF [auth b],
TG [auth c],
UB [auth B],
UF [auth b],
UG [auth c],
VB [auth B],
VF [auth b],
WB [auth B],
WF [auth b],
XF [auth b],
YF [auth b],
ZF [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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DB [auth A],
FD [auth D],
FF [auth a],
HH [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AC [auth B]
DG [auth b]
ME [auth X]
OI [auth x]
WA [auth A]
AC [auth B],
DG [auth b],
ME [auth X],
OI [auth x],
WA [auth A],
XA [auth A],
YE [auth a],
ZE [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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BH [auth c]
DD [auth C]
EC [auth B]
FH [auth c]
GD [auth D]
BH [auth c],
DD [auth C],
EC [auth B],
FH [auth c],
GD [auth D],
HG [auth b],
IH [auth d],
MD [auth D],
OH [auth d],
VA [auth A],
XD [auth H],
XE [auth a],
ZC [auth C],
ZH [auth h]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

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LD [auth D],
NH [auth d],
TA [auth A],
VE [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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FB [auth A]
GE [auth L]
HF [auth a]
II [auth l]
ND [auth D]
FB [auth A],
GE [auth L],
HF [auth a],
II [auth l],
ND [auth D],
OD [auth D],
PD [auth D],
PH [auth d],
QH [auth d],
RH [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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

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WD [auth E],
YH [auth e]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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AG [auth b]
AI [auth h]
BG [auth b]
CG [auth b]
DE [auth K]
AG [auth b],
AI [auth h],
BG [auth b],
CG [auth b],
DE [auth K],
FE [auth K],
FI [auth k],
HI [auth k],
JE [auth T],
KD [auth D],
MH [auth d],
MI [auth t],
SA [auth A],
TC [auth C],
UC [auth C],
UE [auth a],
VG [auth c],
WG [auth c],
XB [auth B],
YB [auth B],
YD [auth H],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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CD [auth C]
CE [auth J]
DC [auth B]
ED [auth C]
EH [auth c]
CD [auth C],
CE [auth J],
DC [auth B],
ED [auth C],
EH [auth c],
EI [auth j],
GG [auth b],
GH [auth c],
IE [auth M],
JI [auth m],
NE [auth Z],
PI [auth z],
VD [auth E],
XH [auth e]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX (Subject of Investigation/LOI)
Query on OEX

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CB [auth A],
EF [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
STE
Query on STE

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AB [auth A]
AD [auth C]
AE [auth I]
BB [auth A]
BC [auth B]
AB [auth A],
AD [auth C],
AE [auth I],
BB [auth A],
BC [auth B],
BD [auth C],
BE [auth J],
BF [auth a],
CC [auth B],
CF [auth a],
CH [auth c],
CI [auth i],
DF [auth a],
DH [auth c],
DI [auth j],
EE [auth K],
EG [auth b],
FC [auth B],
FG [auth b],
GB [auth A],
GI [auth k],
HE [auth M],
IF [auth a],
JF [auth b],
KE [auth T],
KI [auth m],
LI [auth t],
QD [auth D],
RD [auth D],
SD [auth E],
SH [auth d],
TD [auth E],
TH [auth d],
UA [auth A],
UD [auth E],
UH [auth e],
VC [auth C],
VH [auth e],
WE [auth a],
WH [auth e],
XG [auth c],
ZA [auth A]
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
BCT
Query on BCT

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

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MA [auth A],
OE [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

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NA [auth A],
OA [auth A],
PE [auth a],
QE [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
AA [auth i],
H [auth I]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2020-03809
Germanys Excellence StrategyGermany2008/1-390540038
German Research Foundation (DFG)GermanySFB1078

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary