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- PDB-7oy8: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex -

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Basic information

Entry
Database: PDB / ID: 7oy8
TitleCryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Components
  • (Antenna complex, alpha/beta ...) x 2
  • (Photosynthetic reaction ...) x 2
  • Light-harvesting protein B-870 beta chain
  • Reaction center protein M chain
KeywordsSTRUCTURAL PROTEIN / photosynthesis / light-harvesting complex / reaction centre / purple bacteria / membrane protein
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 / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane / metal ion binding / 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 / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / 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
Trans-Geranyl BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / Chem-CD4 / SPIRILLOXANTHIN / : / Chem-PGW / PHOSPHATE ION / Chem-RQ0 / UBIQUINONE-10 / Light-harvesting protein B-870 beta chain ...Trans-Geranyl BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / Chem-CD4 / SPIRILLOXANTHIN / : / Chem-PGW / PHOSPHATE ION / Chem-RQ0 / UBIQUINONE-10 / Light-harvesting protein B-870 beta chain / Antenna complex, alpha/beta subunit / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center, H-chain
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsQian, P. / Croll, T.I. / Castro, H.P. / Moriarty, N.W. / sader, K. / Hunter, C.N.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1 United Kingdom
European Research Council (ERC)Synergy Award 854126European Union
Wellcome Trust209407/Z/17/Z United Kingdom
CitationJournal: Biochem J / Year: 2021
Title: Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex at 2.5 Å.
Authors: Pu Qian / Tristan I Croll / David J K Swainsbury / Pablo Castro-Hartmann / Nigel W Moriarty / Kasim Sader / C Neil Hunter /
Abstract: The reaction centre light-harvesting 1 (RC-LH1) complex is the core functional component of bacterial photosynthesis. We determined the cryo-electron microscopy (cryo-EM) structure of the RC-LH1 ...The reaction centre light-harvesting 1 (RC-LH1) complex is the core functional component of bacterial photosynthesis. We determined the cryo-electron microscopy (cryo-EM) structure of the RC-LH1 complex from Rhodospirillum rubrum at 2.5 Å resolution, which reveals a unique monomeric bacteriochlorophyll with a phospholipid ligand in the gap between the RC and LH1 complexes. The LH1 complex comprises a circular array of 16 αβ-polypeptide subunits that completely surrounds the RC, with a preferential binding site for a quinone, designated QP, on the inner face of the encircling LH1 complex. Quinols, initially generated at the RC QB site, are proposed to transiently occupy the QP site prior to traversing the LH1 barrier and diffusing to the cytochrome bc1 complex. Thus, the QP site, which is analogous to other such sites in recent cryo-EM structures of RC-LH1 complexes, likely reflects a general mechanism for exporting quinols from the RC-LH1 complex.
History
DepositionJun 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_validate_chiral
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
1: Light-harvesting protein B-870 beta chain
2: Antenna complex, alpha/beta subunit
3: Light-harvesting protein B-870 beta chain
4: Antenna complex, alpha/beta subunit
5: Light-harvesting protein B-870 beta chain
6: Antenna complex, alpha/beta subunit
7: Light-harvesting protein B-870 beta chain
8: Antenna complex, alpha/beta subunit
9: Light-harvesting protein B-870 beta chain
A: Antenna complex, alpha/beta subunit
D: Antenna complex, alpha/beta subunit
E: Antenna complex, alpha/beta subunit
F: Antenna complex, alpha/beta subunit
G: Antenna complex, alpha/beta subunit
H: Photosynthetic reaction center, H-chain
I: Light-harvesting protein B-870 beta chain
J: Antenna complex, alpha/beta subunit
K: Light-harvesting protein B-870 beta chain
L: Photosynthetic reaction center L subunit
M: Reaction center protein M chain
N: Antenna complex, alpha/beta subunit
O: Light-harvesting protein B-870 beta chain
Q: Light-harvesting protein B-870 beta chain
R: Antenna complex, alpha/beta subunit
S: Light-harvesting protein B-870 beta chain
T: Antenna complex, alpha/beta subunit
U: Light-harvesting protein B-870 beta chain
V: Antenna complex, alpha/beta subunit
W: Light-harvesting protein B-870 beta chain
X: Antenna complex, alpha/beta subunit
Y: Light-harvesting protein B-870 beta chain
Z: Antenna complex, alpha/beta subunit
d: Light-harvesting protein B-870 beta chain
m: Light-harvesting protein B-870 beta chain
n: Light-harvesting protein B-870 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,533103
Polymers286,14235
Non-polymers53,39168
Water6,702372
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area157910 Å2
ΔGint-1034 kcal/mol
Surface area91030 Å2

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Components

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Protein , 2 types, 17 molecules 13579IKOQSUWYdmnM

#1: Protein
Light-harvesting protein B-870 beta chain / Antenna pigment protein beta chain / LH-1


Mass: 6083.941 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
References: UniProt: Q2RQ23
#5: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34234.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
References: UniProt: Q2RQ26

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Antenna complex, alpha/beta ... , 2 types, 16 molecules 2468ADEFGJNTVXZR

#2: Protein/peptide
Antenna complex, alpha/beta subunit


Mass: 5920.986 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
References: UniProt: Q2RQ24
#6: Protein Antenna complex, alpha/beta subunit


Mass: 7112.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
References: UniProt: Q2RQ24

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Photosynthetic reaction ... , 2 types, 2 molecules HL

#3: Protein Photosynthetic reaction center, H-chain


Mass: 27976.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
References: UniProt: Q2RWS4
#4: Protein Photosynthetic reaction center L subunit / Reaction center protein L chain


Mass: 30660.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
References: UniProt: Q2RQ25

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Sugars , 1 types, 1 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 11 types, 439 molecules

#7: Chemical...
ChemComp-07D / Trans-Geranyl BACTERIOCHLOROPHYLL A


Mass: 901.425 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C55H64MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O2
#9: Chemical ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL


Mass: 749.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#10: Chemical ChemComp-CD4 / (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate / tetramyristoyl-cardiolipin


Mass: 1241.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C65H126O17P2
#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-RQ0 / 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione


Mass: 844.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C58H85NO3 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#15: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#16: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: RC-LH1 from rhodospirillum rubrum / Type: COMPLEX
Details: A reaction centre light harvesting core complex from purple bacterium ops. rubrum.
Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 297.7 kDa/nm / Experimental value: YES
Source (natural)Organism: Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Strain: S1
Buffer solutionpH: 8 / Details: 20 mM HEPES, 0.03% beta DDM, pH 8.0
Buffer componentConc.: 20 mM / Name: HEPES / Formula: C8H18N2O4S
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The protein were solubilised using detergent beta DDM, and purified by the use of ion exchange column and size exclusion column. Monodisperse sample was used for cry-EM preparation.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Quantifiol R1.2/1.3 grid, glow discharged. bloting time: 2.5, bloting force 3, waiting time 0

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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 magnification: 120000 X / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12.12 sec. / Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9024
Details: total dose of 45 was fractionated to 42 frames within 12.12 second.

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_4234refinement
PHENIXdev_4234refinement
EM software
IDNameVersionCategory
1cisTEM1particle selection
2EPU10.2image acquisition
4CTFFINDCTF correction
7ISOLDEmodel fitting
9EMAN2initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
Image processingDetails: Images were motion corrected and CTF corrected.
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1519688
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 519005 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11LGH

1lgh

11LGH1PDBexperimental model
23I4D

3i4d

13I4D2PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 27.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003523479
ELECTRON MICROSCOPYf_angle_d0.951932369
ELECTRON MICROSCOPYf_chiral_restr0.04723071
ELECTRON MICROSCOPYf_plane_restr0.00783582
ELECTRON MICROSCOPYf_dihedral_angle_d15.12557921

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