7CZL

Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium Thermosynechococcus vulcanus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium Thermosynechococcus vulcanus .

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

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2018053118
  • Primary Citation of Related Structures:  
    7CZL

  • PubMed Abstract: 

    Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyzes light-driven water oxidation, leading to the conversion of light energy into chemical energy and the release of molecular oxygen. Psb27 is a small thylakoid lumen-localized protein known to serve as an assembly factor for the biogenesis and repair of the PSII complex. The exact location and binding fashion of Psb27 in the intermediate PSII remain elusive. Here, we report the structure of a dimeric Psb27-PSII complex purified from a psbV deletion mutant (ΔPsbV) of the cyanobacterium Thermosynechococcus vulcanus , solved by cryo-electron microscopy. Our structure showed that Psb27 is associated with CP43 at the luminal side, with specific interactions formed between Helix 2 and Helix 3 of Psb27 and a loop region between Helix 3 and Helix 4 of CP43 (loop C) as well as the large, lumen-exposed and hydrophilic E-loop of CP43. The binding of Psb27 imposes some conflicts with the N-terminal region of PsbO and also induces some conformational changes in CP43, CP47, and D2. This makes PsbO unable to bind in the Psb27-PSII. Conformational changes also occurred in D1, PsbE, PsbF, and PsbZ; this, together with the conformational changes occurred in CP43, CP47, and D2, may prevent the binding of PsbU and induce dissociation of PsbJ. This structural information provides important insights into the regulation mechanism of Psb27 in the biogenesis and repair of PSII.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084 Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
N [auth a]
324Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P51765 (Thermostichus vulcanus)
Explore P51765 
Go to UniProtKB:  P51765
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51765
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
O [auth b]
505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus)
Explore D0VWR1 
Go to UniProtKB:  D0VWR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
P [auth c]
446Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR7 (Thermostichus vulcanus)
Explore D0VWR7 
Go to UniProtKB:  D0VWR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
Q [auth d]
339Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR8 (Thermostichus vulcanus)
Explore D0VWR8 
Go to UniProtKB:  D0VWR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
R [auth e]
65Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12238 (Thermostichus vulcanus)
Explore P12238 
Go to UniProtKB:  P12238
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12238
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
S [auth f]
31Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12239 (Thermostichus vulcanus)
Explore P12239 
Go to UniProtKB:  P12239
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12239
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
T [auth h]
62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19052 (Thermostichus vulcanus)
Explore P19052 
Go to UniProtKB:  P19052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19052
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I],
U [auth i]
34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12240 (Thermostichus vulcanus)
Explore P12240 
Go to UniProtKB:  P12240
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12240
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KI [auth K],
V [auth k]
37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19054 (Thermostichus vulcanus)
Explore P19054 
Go to UniProtKB:  P19054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19054
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJ [auth L],
W [auth l]
37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12241 (Thermostichus vulcanus)
Explore P12241 
Go to UniProtKB:  P12241
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12241
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MK [auth M],
X [auth m]
33Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12312 (Thermostichus vulcanus)
Explore P12312 
Go to UniProtKB:  P12312
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12312
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TL [auth T],
Y [auth t]
30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12313 (Thermostichus vulcanus)
Explore P12313 
Go to UniProtKB:  P12313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12313
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZM [auth Z],
Z [auth z]
62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus)
Explore D0VWR5 
Go to UniProtKB:  D0VWR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12AA [auth Y],
DA [auth y]
30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus)
Explore D0VWR3 
Go to UniProtKB:  D0VWR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Psb27BA [auth n],
CA [auth N]
108Thermostichus vulcanusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XEA [auth X],
FA [auth x]
40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus)
Explore D0VWR4 
Go to UniProtKB:  D0VWR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
CC [auth C]
DC [auth C]
EC [auth C]
ID [auth a]
IF [auth h]
CC [auth C],
DC [auth C],
EC [auth C],
ID [auth a],
IF [auth h],
SE [auth c],
TC [auth H],
TE [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AB [auth B]
AD [auth a]
BB [auth B]
BD [auth a]
CB [auth B]
AB [auth B],
AD [auth a],
BB [auth B],
BD [auth a],
CB [auth B],
DB [auth B],
DD [auth a],
EB [auth B],
EE [auth c],
FB [auth B],
FE [auth c],
GA [auth A],
GB [auth B],
GE [auth c],
HA [auth A],
HB [auth B],
HE [auth c],
IA [auth A],
IE [auth c],
JE [auth c],
JF [auth k],
KA [auth A],
KC [auth D],
KD [auth b],
KE [auth c],
LC [auth D],
LD [auth b],
LE [auth c],
MB [auth C],
MD [auth b],
ME [auth c],
NB [auth C],
ND [auth b],
NE [auth c],
OB [auth C],
OD [auth b],
OE [auth c],
PB [auth C],
PD [auth b],
PE [auth c],
QB [auth C],
QD [auth b],
RB [auth C],
RD [auth b],
SA [auth B],
SB [auth C],
SD [auth b],
TA [auth B],
TB [auth C],
TD [auth b],
UA [auth B],
UB [auth C],
UD [auth b],
VA [auth B],
VB [auth C],
VD [auth b],
WA [auth B],
WB [auth C],
WD [auth b],
XA [auth B],
XB [auth C],
XD [auth b],
YA [auth B],
YB [auth C],
YD [auth b],
YE [auth d],
ZA [auth B],
ZC [auth a],
ZD [auth b],
ZE [auth d]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

Download Ideal Coordinates CCD File 
CD [auth a],
IC [auth D],
JA [auth A],
XE [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

Download Ideal Coordinates CCD File 
CF [auth d]
JC [auth D]
MF [auth l]
PA [auth A]
UC [auth L]
CF [auth d],
JC [auth D],
MF [auth l],
PA [auth A],
UC [auth L],
YC [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
LHG
Query on LHG

Download Ideal Coordinates CCD File 
GD [auth a],
NA [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
MGE
Query on MGE

Download Ideal Coordinates CCD File 
DE [auth b]
DF [auth d]
EF [auth d]
FC [auth C]
FF [auth d]
DE [auth b],
DF [auth d],
EF [auth d],
FC [auth C],
FF [auth d],
KB [auth B],
LF [auth l],
NF [auth m],
OC [auth D],
PC [auth D],
PF [auth m],
QC [auth D],
RA [auth A],
UE [auth c]
(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 
GF [auth f],
RC [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PQ9
Query on PQ9

Download Ideal Coordinates CCD File 
AF [auth d],
ED [auth a],
LA [auth A],
MC [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 
AC [auth C]
AE [auth b]
BC [auth C]
BE [auth b]
BF [auth d]
AC [auth C],
AE [auth b],
BC [auth C],
BE [auth b],
BF [auth d],
CE [auth b],
FD [auth a],
HF [auth h],
IB [auth B],
JB [auth B],
KF [auth k],
MA [auth A],
NC [auth D],
QE [auth c],
QF [auth t],
RE [auth c],
RF [auth t],
SC [auth H],
SF [auth z],
TF [auth Y],
XC [auth T],
ZB [auth C]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
HD [auth a]
LB [auth B]
OA [auth A]
OF [auth m]
VC [auth M]
HD [auth a],
LB [auth B],
OA [auth A],
OF [auth m],
VC [auth M],
WC [auth T]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

Download Ideal Coordinates CCD File 
JD [auth a],
QA [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
HC [auth D],
WE [auth d]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
GC [auth C],
VE [auth c]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
UF [auth n],
VF [auth N]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references