7D1U | pdb_00007d1u

Cryo-EM Structure of PSII at 2.08 angstrom resolution

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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


Literature

High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.

Kato, K., Miyazaki, N., Hamaguchi, T., Nakajima, Y., Akita, F., Yonekura, K., Shen, J.R.

(2021) Commun Biol 4: 382-382

  • DOI: https://doi.org/10.1038/s42003-021-01919-3
  • Primary Citation of Related Structures:  
    7D1T, 7D1U

  • PubMed Abstract: 

    Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

    • Organizational Affiliation: 
    • Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
U [auth a]		334Thermostichus vulcanusMutation(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,
V [auth b]		505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
W [auth c]		451Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]		342Thermostichus vulcanusMutation(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,
Y [auth e]		81Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]		34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]		63Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth i],
H [auth I]		36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth j],
I [auth J]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7DGD4 (Thermostichus vulcanus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth k],
J [auth K]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth l],
K [auth L]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth m],
L [auth M]		34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth o],
M [auth O]		244Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth t],
N [auth T]		31Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth u],
O [auth U]		97Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56152 (Thermostichus vulcanus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]		137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth y],
Q [auth Y]		30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XLA [auth x],
R [auth X]		40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZMA [auth z],
S [auth Z]		62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YNA [auth r],
T [auth R]		34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0DM37 (Thermostichus vulcanus)
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Small Molecules
Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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LH [auth h]
OG [auth c]
PG [auth c]
QG [auth c]
RD [auth H]
LH [auth h],
OG [auth c],
PG [auth c],
QG [auth c],
RD [auth H],
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]
BD [auth D]
BF [auth b]
BG [auth c]
AF [auth b],
AG [auth c],
BD [auth D],
BF [auth b],
BG [auth c],
CB [auth B],
CF [auth b],
CG [auth c],
DB [auth B],
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],
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],
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],
SA [auth A],
TA [auth A],
VA [auth A],
VG [auth d],
XG [auth d],
YG [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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CD [auth D],
PE [auth a],
UA [auth A],
WG [auth d]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD
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BH [auth d]
HD [auth D]
SE [auth a]
TH [auth l]
UE [auth a]
BH [auth d],
HD [auth D],
SE [auth a],
TH [auth l],
UE [auth a],
XA [auth A],
ZA [auth A],
ZD [auth L]
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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EC [auth C]
FH [auth d]
LD [auth D]
RG [auth c]
SF [auth b]
EC [auth C],
FH [auth d],
LD [auth D],
RG [auth c],
SF [auth b],
TG [auth c],
VB [auth B],
XC [auth C],
YF [auth c],
ZC [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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AH [auth d],
GD [auth D],
TE [auth a],
YA [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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AC [auth B]
CH [auth d]
DH [auth d]
EH [auth d]
HH [auth e]
AC [auth B],
CH [auth d],
DH [auth d],
EH [auth d],
HH [auth e],
ID [auth D],
JD [auth D],
KD [auth D],
ND [auth E],
XF [auth b]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC
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FE [auth V],
YH [auth v]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM
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JH [auth e],
PD [auth E]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX
Query on RRX
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KH [auth h],
QD [auth H]		(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR
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CC [auth B]
CE [auth T]
FD [auth D]
GE [auth Y]
MG [auth c]
CC [auth B],
CE [auth T],
FD [auth D],
GE [auth Y],
MG [auth c],
NG [auth c],
PF [auth b],
QF [auth b],
RE [auth a],
RF [auth b],
SB [auth B],
SC [auth C],
SG [auth c],
TB [auth B],
TC [auth C],
UB [auth B],
WA [auth A],
YC [auth C],
ZG [auth d],
ZH [auth y]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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AE [auth M]
BI [auth z]
IE [auth Z]
NH [auth i]
QH [auth j]
AE [auth M],
BI [auth z],
IE [auth Z],
NH [auth i],
QH [auth j],
TD [auth I],
VH [auth m],
WD [auth J]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX
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JE [auth a],
OA [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT
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BB [auth A],
WE [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
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KE [auth a],
PA [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL
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LE [auth a],
ME [auth a],
QA [auth A],
RA [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
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PH [auth j],
VD [auth J]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL
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AB [auth A]
AD [auth C]
AI [auth x]
BC [auth B]
BE [auth M]
AB [auth A],
AD [auth C],
AI [auth x],
BC [auth B],
BE [auth M],
DC [auth B],
DE [auth T],
EE [auth T],
GH [auth d],
HE [auth X],
IH [auth e],
MD [auth D],
MH [auth i],
OD [auth E],
OH [auth i],
RH [auth j],
SD [auth I],
SH [auth k],
TF [auth b],
UD [auth I],
UF [auth b],
UG [auth c],
UH [auth m],
VE [auth a],
VF [auth b],
WB [auth B],
WF [auth b],
WH [auth t],
XB [auth B],
XD [auth J],
XE [auth b],
XH [auth t],
YB [auth B],
YD [auth K],
YE [auth b],
ZB [auth B]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HSK
Query on HSK		D,
X [auth d]		L-PEPTIDE LINKINGC6 H9 N3 O3HIS
FME
Query on FME		BA [auth i],
H [auth I]		L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 2.0: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 3.0: 2025-07-30
    Changes: Atomic model, Data collection, Derived calculations