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- PDB-7ddq: Structure of RC-LH1-PufX from Rhodobacter veldkampii -

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Entry
Database: PDB / ID: 7ddq
TitleStructure of RC-LH1-PufX from Rhodobacter veldkampii
Components
  • (Antenna pigment protein ...) x 2
  • (Photosynthetic reaction center ...) x 2
  • PufX
  • Reaction center protein M chain
KeywordsPHOTOSYNTHESIS / membrane protein / light-harvesting / reaction center / pufx
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 / metal ion binding / membrane / plasma membrane
Similarity search - Function
Light-harvesting complex / Light-harvesting Protein / 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. / Photosynthetic Reaction Center; Chain H, domain 2 ...Light-harvesting complex / Light-harvesting Protein / 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. / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / 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, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / 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. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / SPHEROIDENE / UBIQUINONE-10 / Antenna pigment protein beta chain / Reaction center protein M chain / PufX / Photosynthetic reaction center subunit H ...1,2-Distearoyl-sn-glycerophosphoethanolamine / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / SPHEROIDENE / UBIQUINONE-10 / Antenna pigment protein beta chain / Reaction center protein M chain / PufX / Photosynthetic reaction center subunit H / Antenna pigment protein alpha chain / Reaction center protein L chain
Similarity search - Component
Biological speciesRhodobacter veldkampii DSM 11550 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsBracun, L. / Yamagata, A. / Shirouzu, M. / Liu, L.N.
Funding support United Kingdom, Japan, 5items
OrganizationGrant numberCountry
Royal Society180030 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)R003890 United Kingdom
Japan Agency for Medical Research and Development (AMED)JP20am0101082 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101115 Japan
Japan Society for the Promotion of Science (JSPS)JP 19H03162 Japan
CitationJournal: Sci Adv / Year: 2021
Title: Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution.
Authors: Laura Bracun / Atsushi Yamagata / Bern M Christianson / Tohru Terada / Daniel P Canniffe / Mikako Shirouzu / Lu-Ning Liu /
Abstract: The reaction center (RC)-light-harvesting complex 1 (LH1) supercomplex plays a pivotal role in bacterial photosynthesis. Many RC-LH1 complexes integrate an additional protein PufX that is key for ...The reaction center (RC)-light-harvesting complex 1 (LH1) supercomplex plays a pivotal role in bacterial photosynthesis. Many RC-LH1 complexes integrate an additional protein PufX that is key for bacterial growth and photosynthetic competence. Here, we present a cryo-electron microscopy structure of the RC-LH1-PufX supercomplex from at 2.8-Å resolution. The RC-LH1-PufX monomer contains an LH ring of 15 αβ-polypeptides with a 30-Å gap formed by PufX. PufX acts as a molecular "cross brace" to reinforce the RC-LH1 structure. The unusual PufX-mediated large opening in the LH1 ring and defined arrangement of proteins and cofactors provide the molecular basis for the assembly of a robust RC-LH1-PufX supercomplex and efficient quinone transport and electron transfer. These architectural features represent the natural strategies for anoxygenic photosynthesis and environmental adaptation.
History
DepositionOct 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
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Revision 1.0Jun 30, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 30, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 30, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 2.0Jul 7, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id
Revision 2.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Jun 25, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
o: Antenna pigment protein alpha chain
N: Antenna pigment protein beta chain
t: Antenna pigment protein alpha chain
S: Antenna pigment protein beta chain
r: Antenna pigment protein alpha chain
O: Antenna pigment protein beta chain
a: Antenna pigment protein alpha chain
U: Antenna pigment protein beta chain
e: Antenna pigment protein alpha chain
D: Antenna pigment protein beta chain
b: Antenna pigment protein alpha chain
A: Antenna pigment protein beta chain
k: Antenna pigment protein alpha chain
J: Antenna pigment protein beta chain
f: Antenna pigment protein alpha chain
E: Antenna pigment protein beta chain
u: Antenna pigment protein alpha chain
T: Antenna pigment protein beta chain
X: PufX
s: Antenna pigment protein alpha chain
R: Antenna pigment protein beta chain
n: Antenna pigment protein alpha chain
K: Antenna pigment protein beta chain
i: Antenna pigment protein alpha chain
G: Antenna pigment protein beta chain
j: Antenna pigment protein alpha chain
I: Antenna pigment protein beta chain
L: Photosynthetic reaction center L subunit
M: Reaction center protein M chain
H: Photosynthetic reaction center subunit H
g: Antenna pigment protein alpha chain
F: Antenna pigment protein beta chain
d: Antenna pigment protein alpha chain
B: Antenna pigment protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,12196
Polymers285,44834
Non-polymers49,67362
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area182360 Å2
ΔGint-1434 kcal/mol
Surface area91320 Å2

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Components

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Antenna pigment protein ... , 2 types, 30 molecules otraebkfusnijgdNSOUDAJETRKGIFB

#1: Protein
Antenna pigment protein alpha chain


Mass: 6699.024 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria)
References: UniProt: A0A2T4JIR4
#2: Protein/peptide
Antenna pigment protein beta chain


Mass: 5551.439 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria)
References: UniProt: A0A2T4JIL7

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Protein , 2 types, 2 molecules XM

#3: Protein PufX


Mass: 8923.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria)
References: UniProt: A0A2T4JIP3
#5: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34425.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria)
References: UniProt: A0A2T4JIN0

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Photosynthetic reaction center ... , 2 types, 2 molecules LH

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


Mass: 30896.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria)
References: UniProt: A0A2T4JIS6
#6: Protein Photosynthetic reaction center subunit H


Mass: 27445.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria)
References: UniProt: A0A2T4JIP4

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Non-polymers , 6 types, 62 molecules

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


Mass: 911.504 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#8: Chemical
ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C41H60O
#9: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C59H90O4
#10: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H76N4O6
#11: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#12: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestN
Has protein modificationN

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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: Photosynthetic core complex featuring reaction center, LH1 and PufX
Type: COMPLEX / Entity ID: #3-#6 / Source: NATURAL
Source (natural)Organism: Rhodobacter veldkampii DSM 11550 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
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: DARK FIELD
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 184921 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00823465
ELECTRON MICROSCOPYf_angle_d1.26832317
ELECTRON MICROSCOPYf_dihedral_angle_d24.6714004
ELECTRON MICROSCOPYf_chiral_restr0.0543244
ELECTRON MICROSCOPYf_plane_restr0.0053949

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