7DXA

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


This is version 2.1 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 of 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.


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))
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UniProt GroupQ8DLJ8
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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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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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UniProt GroupP51765
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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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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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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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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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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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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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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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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)
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UniProt GroupP12312
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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)
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UniProt GroupP12313
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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)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified transmembrane proteinN [auth C]23Thermostichus vulcanusMutation(s): 0 
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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FB [auth d]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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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

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R [auth a],
S [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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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

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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

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GB [auth e]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PQ9
Query on PQ9

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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

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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

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KB [auth t],
TA [auth b],
VA [auth d]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
HTG
Query on HTG

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EB [auth d]heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
FE2
Query on FE2

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WA [auth d]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

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V [auth a]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL
Query on UNL

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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 

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