7D1T image
Entry Detail
PDB ID:
7D1T
EMDB ID:
Keywords:
Title:
Cryo-EM Structure of PSII at 1.95 angstrom resolution
Biological Source:
PDB Version:
Deposition Date:
2020-09-15
Release Date:
2021-03-31
Method Details:
Experimental Method:
Resolution:
1.95 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Photosystem II protein D1
Chain IDs:A, U (auth: a)
Chain Length:334
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II CP47 reaction center protein
Chain IDs:B, V (auth: b)
Chain Length:505
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II CP43 reaction center protein
Chain IDs:C, W (auth: c)
Chain Length:451
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II D2 protein
Chain IDs:D, X (auth: d)
Chain Length:342
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit alpha
Chain IDs:E, Y (auth: e)
Chain Length:81
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit beta
Chain IDs:F, Z (auth: f)
Chain Length:34
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein H
Chain IDs:G (auth: H), AA (auth: h)
Chain Length:63
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein I
Chain IDs:H (auth: I), BA (auth: i)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein J
Chain IDs:I (auth: J), CA (auth: j)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein K
Chain IDs:J (auth: K), DA (auth: k)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein L
Chain IDs:K (auth: L), EA (auth: l)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein M
Chain IDs:L (auth: M), FA (auth: m)
Chain Length:34
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II manganese-stabilizing polypeptide
Chain IDs:M (auth: O), GA (auth: o)
Chain Length:244
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II protein Y
Chain IDs:T (auth: R), NA (auth: r)
Chain Length:34
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein T
Chain IDs:N (auth: T), HA (auth: t)
Chain Length:31
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II 12 kDa extrinsic protein
Chain IDs:O (auth: U), IA (auth: u)
Chain Length:97
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Cytochrome c-550
Chain IDs:P (auth: V), JA (auth: v)
Chain Length:137
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein X
Chain IDs:R (auth: X), LA (auth: x)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Ycf12
Chain IDs:Q (auth: Y), KA (auth: y)
Chain Length:30
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Z
Chain IDs:S (auth: Z), MA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME H MET modified residue
HSK D HIS modified residue
Primary Citation
High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.
Commun Biol 4 382 382 (2021)
PMID: 33753866 DOI: 10.1038/s42003-021-01919-3

Abstact

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.

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