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- PDB-7vb9: Rba sphaeroides PufY-KO RC-LH1 dimer type-2 -

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Basic information

Entry
Database: PDB / ID: 7vb9
TitleRba sphaeroides PufY-KO RC-LH1 dimer type-2
Components
  • (Light-harvesting protein B-875 ...) x 2
  • (Reaction center protein ...) x 3
  • Intrinsic membrane protein PufX
KeywordsPHOTOSYNTHESIS / dimer / PufY-KO / mutant / photosystem
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 / 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
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsBracun, L. / Yamagata, A. / Liu, L.N. / Shirouzu, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society United Kingdom
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
DepositionAug 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
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
C: Intrinsic membrane protein PufX
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
x: Light-harvesting protein B-875 beta chain
y: Light-harvesting protein B-875 alpha chain
z: Light-harvesting protein B-875 beta chain
5: Light-harvesting protein B-875 alpha chain
4: Light-harvesting protein B-875 beta chain
6: Light-harvesting protein B-875 alpha chain
aa: Light-harvesting protein B-875 beta chain
Q: Light-harvesting protein B-875 alpha chain
ab: Light-harvesting protein B-875 beta chain
c: Intrinsic membrane protein PufX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)556,331158
Polymers473,66651
Non-polymers82,665107
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
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, 43 molecules ADFIKO79adfikoqsuwy56QBEGJN80b...

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


Mass: 6816.169 Da / Num. of mol.: 22 / 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.: 21 / 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 , 1 types, 2 molecules Cc

#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

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Non-polymers , 7 types, 107 molecules

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


Mass: 911.504 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-BPH / BACTERIOPHEOPHYTIN A


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


Mass: 863.343 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical...
ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C41H60O / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#13: 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.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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Details

Has ligand of interestY

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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: Rhodobacter sphaeroides PufY-KO RC-LH1 dimer type-2 / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain: Rsp_7571 KO
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.868 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53830 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 33.54 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006837888
ELECTRON MICROSCOPYf_angle_d0.843352075
ELECTRON MICROSCOPYf_chiral_restr0.04175347
ELECTRON MICROSCOPYf_plane_restr0.00386155
ELECTRON MICROSCOPYf_dihedral_angle_d20.26212813

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