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- PDB-7vor: The structure of dimeric photosynthetic RC-LH1 supercomplex in Class-1 -

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Basic information

Entry
Database: PDB / ID: 7vor
TitleThe structure of dimeric photosynthetic RC-LH1 supercomplex in Class-1
Components
  • (Light-harvesting protein B-875 ...) x 2
  • (Reaction center protein ...) x 3
  • Intrinsic membrane protein PufX
  • Rsp_7571 Protein-Y PufY
KeywordsPHOTOSYNTHESIS / SUPERCOMPLEX / purple bacteria
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / photosynthesis / metal ion binding / membrane / plasma membrane
Similarity search - Function
Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily ...Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / SPHEROIDENE / UBIQUINONE-10 / Intrinsic membrane protein PufX / Reaction center protein H chain / Light-harvesting protein B-875 beta chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / SPHEROIDENE / UBIQUINONE-10 / Intrinsic membrane protein PufX / Reaction center protein H chain / Light-harvesting protein B-875 beta chain / Light-harvesting protein B-875 alpha chain / Reaction center protein L chain / Reaction center protein M chain / Uncharacterized protein
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsCao, P. / Li, M. / Liu, L.N.
Funding support China, United Kingdom, 7items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB27020106 China
Chinese Academy of SciencesXDB37020101 China
National Natural Science Foundation of China (NSFC)32011530168 China
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R003890/1 and BB/V009729/1 United Kingdom
National Natural Science Foundation of China (NSFC)32070259 China
National Natural Science Foundation of China (NSFC)31930064 China
National Natural Science Foundation of China (NSFC)32070109 China
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.
Authors: Peng Cao / Laura Bracun / Atsushi Yamagata / Bern M Christianson / Tatsuki Negami / Baohua Zou / Tohru Terada / Daniel P Canniffe / Mikako Shirouzu / Mei Li / Lu-Ning Liu /
Abstract: The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species ...The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species possess the dimeric RC-LH1 complex with a transmembrane polypeptide PufX, representing the largest photosynthetic complex in anoxygenic phototrophs. However, the details of the architecture and assembly mechanism of the RC-LH1 dimer are unclear. Here we report seven cryo-electron microscopy (cryo-EM) structures of RC-LH1 supercomplexes from Rhodobacter sphaeroides. Our structures reveal that two PufX polypeptides are positioned in the center of the S-shaped RC-LH1 dimer, interlocking association between the components and mediating RC-LH1 dimerization. Moreover, we identify another transmembrane peptide, designated PufY, which is located between the RC and LH1 subunits near the LH1 opening. PufY binds a quinone molecule and prevents LH1 subunits from completely encircling the RC, creating a channel for quinone/quinol exchange. Genetic mutagenesis, cryo-EM structures, and computational simulations provide a mechanistic understanding of the assembly and electron transport pathways of the RC-LH1 dimer and elucidate the roles of individual components in ensuring the structural and functional integrity of the photosynthetic supercomplex.
History
DepositionOct 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Author supporting evidence / Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_audit_support
Item: _pdbx_audit_support.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Reaction center protein H chain
A: Light-harvesting protein B-875 alpha chain
B: Light-harvesting protein B-875 beta chain
D: Light-harvesting protein B-875 alpha chain
E: Light-harvesting protein B-875 beta chain
F: Light-harvesting protein B-875 alpha chain
G: Light-harvesting protein B-875 beta chain
I: Light-harvesting protein B-875 alpha chain
J: Light-harvesting protein B-875 beta chain
K: Light-harvesting protein B-875 alpha chain
N: Light-harvesting protein B-875 beta chain
O: Light-harvesting protein B-875 alpha chain
P: Light-harvesting protein B-875 beta chain
Q: Light-harvesting protein B-875 alpha chain
R: Light-harvesting protein B-875 beta chain
S: Light-harvesting protein B-875 alpha chain
T: Light-harvesting protein B-875 beta chain
U: Light-harvesting protein B-875 alpha chain
V: Light-harvesting protein B-875 beta chain
W: Light-harvesting protein B-875 alpha chain
C: Light-harvesting protein B-875 beta chain
3: Light-harvesting protein B-875 alpha chain
Z: Light-harvesting protein B-875 beta chain
1: Light-harvesting protein B-875 alpha chain
2: Light-harvesting protein B-875 beta chain
7: Light-harvesting protein B-875 alpha chain
8: Light-harvesting protein B-875 beta chain
9: Light-harvesting protein B-875 alpha chain
0: Light-harvesting protein B-875 beta chain
X: Intrinsic membrane protein PufX
Y: Rsp_7571 Protein-Y PufY
l: Reaction center protein L chain
m: Reaction center protein M chain
h: Reaction center protein H chain
a: Light-harvesting protein B-875 alpha chain
b: Light-harvesting protein B-875 beta chain
d: Light-harvesting protein B-875 alpha chain
e: Light-harvesting protein B-875 beta chain
f: Light-harvesting protein B-875 alpha chain
g: Light-harvesting protein B-875 beta chain
i: Light-harvesting protein B-875 alpha chain
j: Light-harvesting protein B-875 beta chain
k: Light-harvesting protein B-875 alpha chain
n: Light-harvesting protein B-875 beta chain
o: Light-harvesting protein B-875 alpha chain
p: Light-harvesting protein B-875 beta chain
q: Light-harvesting protein B-875 alpha chain
r: Light-harvesting protein B-875 beta chain
s: Light-harvesting protein B-875 alpha chain
t: Light-harvesting protein B-875 beta chain
u: Light-harvesting protein B-875 alpha chain
v: Light-harvesting protein B-875 beta chain
w: Light-harvesting protein B-875 alpha chain
c: Light-harvesting protein B-875 beta chain
5: Light-harvesting protein B-875 alpha chain
z: Light-harvesting protein B-875 beta chain
b1: Light-harvesting protein B-875 alpha chain
4: Light-harvesting protein B-875 beta chain
6: Light-harvesting protein B-875 alpha chain
b8: Light-harvesting protein B-875 beta chain
b9: Light-harvesting protein B-875 alpha chain
b0: Light-harvesting protein B-875 beta chain
x: Intrinsic membrane protein PufX
y: Rsp_7571 Protein-Y PufY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)680,087214
Polymers564,82166
Non-polymers115,267148
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Reaction center protein ... , 3 types, 6 molecules LlMmHh

#1: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31477.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A5
#2: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34529.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A6
#3: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 28066.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J170

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Light-harvesting protein B-875 ... , 2 types, 56 molecules ADFIKOQSUW3179adfikoqsuw5b16b9BE...

#4: Protein ...
Light-harvesting protein B-875 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 6816.169 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A4
#5: Protein/peptide ...
Light-harvesting protein B-875 beta chain / Antenna pigment protein beta chain / LH-3A


Mass: 5592.361 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A3

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Protein , 2 types, 4 molecules XxYy

#6: Protein Intrinsic membrane protein PufX


Mass: 9061.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: P13402
#7: Protein Rsp_7571 Protein-Y PufY


Mass: 5555.558 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: ATH 2.4.1. / References: UniProt: U5NME9

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Non-polymers , 7 types, 148 molecules

#8: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#9: Chemical
ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H76N4O6
#10: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C59H90O4
#11: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#12: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#13: Chemical...
ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: C41H60O
#14: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The dimeric photosynthetic RC-LH1 supercomplex in Class1
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145392 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00646700
ELECTRON MICROSCOPYf_angle_d0.86864156
ELECTRON MICROSCOPYf_dihedral_angle_d14.39316078
ELECTRON MICROSCOPYf_chiral_restr0.1016244
ELECTRON MICROSCOPYf_plane_restr0.0047918

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