7DXA | pdb_00007dxa

PSII intermediate Psb28-RC47


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063.

Xiao, Y.Huang, G.You, X.Zhu, Q.Wang, W.Kuang, T.Han, G.Sui, S.F.Shen, J.R.

(2021) Nat Plants 7: 1132-1142

  • DOI: https://doi.org/10.1038/s41477-021-00961-7
  • Primary Citation Related Structures: 
    7DXA, 7DXH

  • PubMed Abstract: 

    Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. We analysed the structures of two Psb28-bound PSII intermediates, Psb28-RC47 and Psb28-PSII, purified from a psbV-deletion strain of the thermophilic cyanobacterium Thermosynechococcus vulcanus, using cryo-electron microscopy. Both Psb28-RC47 and Psb28-PSII bind one Psb28, one Tsl0063 and an unknown subunit. Psb28 is located at the cytoplasmic surface of PSII and interacts with D1, D2 and CP47, whereas Tsl0063 is a transmembrane subunit and binds at the side of CP47/PsbH. Substantial structural perturbations are observed at the acceptor side, which result in conformational changes of the quinone (Q B ) and non-haem iron binding sites and thus may protect PSII from photodamage during assembly. These results provide a solid structural basis for understanding the assembly process of native PSII.


  • Organizational Affiliation
    • Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 232.92 kDa 
  • Atom Count: 15,162 
  • Modeled Residue Count: 1,629 
  • Deposited Residue Count: 1,779 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center Psb28 protein116Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DLJ8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DLJ8 
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UniProt GroupQ8DLJ8
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tsl0063 protein56Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DMP8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DMP8
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1C [auth a]360Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P51765 (Thermostichus vulcanus)
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Entity Groups
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UniProt GroupP51765
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinD [auth b]505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus)
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UniProt GroupD0VWR1
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinE [auth d]342Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR8 (Thermostichus vulcanus)
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UniProt GroupD0VWR8
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaF [auth e]84Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12238 (Thermostichus vulcanus)
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UniProt GroupP12238
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaG [auth f]45Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12239 (Thermostichus vulcanus)
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UniProt GroupP12239
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HH [auth h]65Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19052 (Thermostichus vulcanus)
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UniProt GroupP19052
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein II [auth i]38Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12240 (Thermostichus vulcanus)
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UniProt GroupP12240
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJ [auth l]37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12241 (Thermostichus vulcanus)
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UniProt GroupP12241
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MK [auth m]36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12312 (Thermostichus vulcanus)
Explore P12312 
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UniProt GroupP12312
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TL [auth t]32Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12313 (Thermostichus vulcanus)
Explore P12313 
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UniProt GroupP12313
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XM [auth x]40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus)
Explore D0VWR4 
Go to UniProtKB:  D0VWR4
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
unidentified transmembrane proteinN [auth C]23Thermostichus vulcanusMutation(s): 0 

Small Molecules

Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
FB [auth d]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth b]
BA [auth b]
CA [auth b]
DA [auth b]
EA [auth b]
AA [auth b],
BA [auth b],
CA [auth b],
DA [auth b],
EA [auth b],
FA [auth b],
GA [auth b],
HA [auth b],
IA [auth b],
JA [auth b],
KA [auth b],
LA [auth b],
MA [auth b],
P [auth a],
Q [auth a],
T [auth a],
UA [auth d],
X [auth b],
XA [auth d],
Y [auth b],
YA [auth d],
Z [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
R [auth a],
S [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
IB [auth l],
O [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
MGE

Query on MGE



Download:Ideal Coordinates CCD File
BB [auth d]
CB [auth d]
DB [auth d]
JB [auth m]
QA [auth b]
BB [auth d],
CB [auth d],
DB [auth d],
JB [auth m],
QA [auth b],
SA [auth b],
W [auth a]
(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
C38 H72 O10
FIJGNIAJTZSERN-DQQGJSMTSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
GB [auth e]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PQ9

Query on PQ9



Download:Ideal Coordinates CCD File
ZA [auth d]5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
C43 H64 O2
JXUCGUASMMLSBH-HOHOQCMASA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AB [auth d]
HB [auth h]
NA [auth b]
OA [auth b]
PA [auth b]
AB [auth d],
HB [auth h],
NA [auth b],
OA [auth b],
PA [auth b],
U [auth a]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
KB [auth t],
TA [auth b],
VA [auth d]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
HTG

Query on HTG



Download:Ideal Coordinates CCD File
EB [auth d]heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
WA [auth d]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
V [auth a]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL

Query on UNL



Download:Ideal Coordinates CCD File
LB [auth x],
RA [auth b]
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 2.0: 2022-04-06
    Changes: Data collection, Database references, Non-polymer description
  • Version 2.1: 2024-06-05
    Changes: Data collection
  • Version 2.2: 2025-07-02
    Changes: Data collection, Structure summary