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- PDB-6z5r: RC-LH1(16) complex from Rhodopseudomonas palustris -

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Basic information

Entry
Database: PDB / ID: 6z5r
TitleRC-LH1(16) complex from Rhodopseudomonas palustris
Components
  • (Light-harvesting complex 1 ...) x 2
  • (Reaction center protein ...) x 2
  • H subunit of photosynthetic reaction center complex
KeywordsPHOTOSYNTHESIS / Reaction center / Light harvesting / Protein W / Quinone
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
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 ...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
Chem-6PL / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / : / Chem-PGT / Chem-QAK / UBIQUINONE-10 / Reaction center protein M chain ...Chem-6PL / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / : / Chem-PGT / Chem-QAK / UBIQUINONE-10 / Reaction center protein M chain / H subunit of photosynthetic reaction center complex / Reaction center protein L chain / Light-harvesting antenna LH1, alpha subunit / Light-harvesting antenna LH1, beta subunit
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSwainsbury, D.J.K. / Qian, P. / Hitchcock, A. / Hunter, C.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1 United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: Structures of RC-LH1 complexes with open or closed quinone channels.
Authors: David J K Swainsbury / Pu Qian / Philip J Jackson / Kaitlyn M Faries / Dariusz M Niedzwiedzki / Elizabeth C Martin / David A Farmer / Lorna A Malone / Rebecca F Thompson / Neil A Ranson / ...Authors: David J K Swainsbury / Pu Qian / Philip J Jackson / Kaitlyn M Faries / Dariusz M Niedzwiedzki / Elizabeth C Martin / David A Farmer / Lorna A Malone / Rebecca F Thompson / Neil A Ranson / Daniel P Canniffe / Mark J Dickman / Dewey Holten / Christine Kirmaier / Andrew Hitchcock / C Neil Hunter /
Abstract: The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes ...The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from A 2.65-Å resolution structure of the RC-LH1-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC Q site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.
History
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
C: Light-harvesting complex 1 alpha chain
D: Light-harvesting complex 1 beta chain
E: Light-harvesting complex 1 alpha chain
F: Light-harvesting complex 1 beta chain
G: Light-harvesting complex 1 alpha chain
I: Light-harvesting complex 1 beta chain
J: Light-harvesting complex 1 alpha chain
K: Light-harvesting complex 1 beta chain
N: Light-harvesting complex 1 alpha chain
O: Light-harvesting complex 1 beta chain
H: H subunit of photosynthetic reaction center complex
L: Reaction center protein L chain
M: Reaction center protein M chain
R: Light-harvesting complex 1 alpha chain
S: Light-harvesting complex 1 beta chain
T: Light-harvesting complex 1 alpha chain
U: Light-harvesting complex 1 beta chain
V: Light-harvesting complex 1 alpha chain
X: Light-harvesting complex 1 beta chain
P: Light-harvesting complex 1 alpha chain
Q: Light-harvesting complex 1 beta chain
Y: Light-harvesting complex 1 alpha chain
Z: Light-harvesting complex 1 beta chain
A: Light-harvesting complex 1 alpha chain
B: Light-harvesting complex 1 beta chain
1: Light-harvesting complex 1 alpha chain
2: Light-harvesting complex 1 beta chain
3: Light-harvesting complex 1 alpha chain
4: Light-harvesting complex 1 beta chain
5: Light-harvesting complex 1 alpha chain
6: Light-harvesting complex 1 beta chain
7: Light-harvesting complex 1 alpha chain
8: Light-harvesting complex 1 beta chain
9: Light-harvesting complex 1 alpha chain
0: Light-harvesting complex 1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,476140
Polymers278,65735
Non-polymers83,819105
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Light-harvesting complex 1 ... , 2 types, 32 molecules CEGJNRTVPYA13579DFIKOSUXQZB24680

#1: Protein/peptide
Light-harvesting complex 1 alpha chain


Mass: 5779.999 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / References: UniProt: Q6N9L4
#2: Protein
Light-harvesting complex 1 beta chain


Mass: 5849.797 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / References: UniProt: Q6N9L5

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Reaction center protein ... , 2 types, 2 molecules LM

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


Mass: 30857.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / References: UniProt: O83005
#5: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34453.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / References: UniProt: A0A4Z7

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Protein / Sugars , 2 types, 13 molecules H

#10: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Protein H subunit of photosynthetic reaction center complex


Mass: 27268.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / References: UniProt: A0A4Z9

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Non-polymers , 10 types, 96 molecules

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


Mass: 911.504 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C42H60O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical...
ChemComp-6PL / (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / 1-PALMITOYL-2-STEAROYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 763.100 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C42H85NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#9: 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.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#11: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-QAK / (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol


Mass: 575.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H78O / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H79O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: Reaction center-Light harvesting complex 1 / Type: COMPLEX
Details: Reaction center-Light harvesting complex 1 from Rhodopseudomonas palustris
Entity ID: #1-#5 / Source: NATURAL
Molecular weightValue: 3.52 MDa / Experimental value: NO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Cellular location: Lamellar membranes
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2200 mMNaClNaCl1
30.03 % w/vn-Dodecyl-beta-D-MaltopyranosideC24H46O111
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 60 % / Chamber temperature: 298 K

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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: 55.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPU2image acquisition
4CTFFIND4.1CTF correctionExecuted within RELION3.0
7Coot0.8.9.2model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 476547 / Details: Autopicked in RELION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260752 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00626025
ELECTRON MICROSCOPYf_angle_d2.77835494
ELECTRON MICROSCOPYf_dihedral_angle_d14.07616033
ELECTRON MICROSCOPYf_chiral_restr0.0493472
ELECTRON MICROSCOPYf_plane_restr0.0053964

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