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- PDB-8bel: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -

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Basic information

Entry
Database: PDB / ID: 8bel
TitleCryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII membrane domain)
Components
  • (Cytochrome b-c1 complex subunit ...) x 5
  • Cytochrome b
  • Cytochrome c1 2, heme protein, mitochondrial
KeywordsMEMBRANE PROTEIN / Plant / Mitochondria / Complex
Function / homology
Function and homology information


vacuole / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane ...vacuole / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / metal ion binding / membrane / cytosol
Similarity search - Function
Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain ...Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-PC7 / Chem-PGT / PHOSPHATIDYLETHANOLAMINE / Chem-Q7G / Chem-UQ5 / UBIQUINONE-7 ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-PC7 / Chem-PGT / PHOSPHATIDYLETHANOLAMINE / Chem-Q7G / Chem-UQ5 / UBIQUINONE-7 / Cytochrome b / Cytochrome b-c1 complex subunit 6-1, mitochondrial / Cytochrome b-c1 complex subunit Rieske-1, mitochondrial / Cytochrome b-c1 complex subunit 10, mitochondrial / Cytochrome c1 2, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 9, mitochondrial / Cytochrome b-c1 complex subunit 8-1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsKlusch, N. / Kuehlbrandt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Plants / Year: 2023
Title: Cryo-EM structure of the respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution.
Authors: Niklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis ...Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III with a co-purified ubiquinone in the Q site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cytochrome b
D: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
E: Cytochrome c1 2, heme protein, mitochondrial
G: Cytochrome b-c1 complex subunit 8-1, mitochondrial
H: Cytochrome b-c1 complex subunit 6-1, mitochondrial
I: Cytochrome b-c1 complex subunit 9, mitochondrial
J: Cytochrome b-c1 complex subunit 10, mitochondrial
M: Cytochrome b
N: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
O: Cytochrome c1 2, heme protein, mitochondrial
Q: Cytochrome b-c1 complex subunit 8-1, mitochondrial
R: Cytochrome b-c1 complex subunit 6-1, mitochondrial
S: Cytochrome b-c1 complex subunit 9, mitochondrial
T: Cytochrome b-c1 complex subunit 10, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,39353
Polymers277,28514
Non-polymers32,10839
Water13,403744
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area88860 Å2
ΔGint-849 kcal/mol
Surface area91980 Å2

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Components

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Protein , 2 types, 4 molecules CMEO

#1: Protein Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 44310.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P42792
#3: Protein Cytochrome c1 2, heme protein, mitochondrial / Complex III subunit 4-2 / Complex III subunit IV-2 / Cytochrome b-c1 complex subunit 4-2 / ...Complex III subunit 4-2 / Complex III subunit IV-2 / Cytochrome b-c1 complex subunit 4-2 / Ubiquinol-cytochrome c reductase complex cytochrome c1 subunit 2 / Cytochrome c-1 2


Mass: 33728.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FKS5

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Cytochrome b-c1 complex subunit ... , 5 types, 10 molecules DNGQHRISJT

#2: Protein Cytochrome b-c1 complex subunit Rieske-1, mitochondrial / Complex III subunit 5-1 / Rieske iron-sulfur protein 1 / RISP1 / Ubiquinol-cytochrome c reductase ...Complex III subunit 5-1 / Rieske iron-sulfur protein 1 / RISP1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit 1


Mass: 29645.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94JS0, quinol-cytochrome-c reductase
#4: Protein Cytochrome b-c1 complex subunit 8-1, mitochondrial / Complex III subunit 8-1 / Complex III subunit VIII / Ubiquinol-cytochrome c oxidoreductase subunit ...Complex III subunit 8-1 / Complex III subunit VIII / Ubiquinol-cytochrome c oxidoreductase subunit 8-1 / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 8517.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SG91
#5: Protein Cytochrome b-c1 complex subunit 6-1, mitochondrial / Complex III subunit 6-1 / Complex III subunit VI / Mitochondrial hinge protein / Ubiquinol- ...Complex III subunit 6-1 / Complex III subunit VI / Mitochondrial hinge protein / Ubiquinol-cytochrome c oxidoreductase subunit 6-1


Mass: 7997.315 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q0WWE3
#6: Protein Cytochrome b-c1 complex subunit 9, mitochondrial / Complex III subunit 9 / Complex III subunit X / Ubiquinol-cytochrome c oxidoreductase subunit 9


Mass: 8461.634 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LXJ2
#7: Protein Cytochrome b-c1 complex subunit 10, mitochondrial / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c oxidoreductase subunit 10


Mass: 5980.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94K78

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Non-polymers , 11 types, 783 molecules

#8: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-UQ5 / 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE


Mass: 522.758 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H50O4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H77O8P / Feature type: SUBJECT OF INVESTIGATION
#11: 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.: 4 / Source method: obtained synthetically / Formula: C40H79O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#12: 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.: 7 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#13: Chemical
ChemComp-PC7 / (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 1-PALMITOYL-2-STEAROYL-PC


Mass: 763.100 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C42H85NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#16: Chemical ChemComp-UQ7 / UBIQUINONE-7


Mass: 658.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H66O4 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-Q7G / 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside


Mass: 1165.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C56H92O25 / Feature type: SUBJECT OF INVESTIGATION
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / 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: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII membrane domain)
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
SpecimenConc.: 0.18 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283.15 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 / Nominal magnification: 215000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
5CTFFIND4.1.13CTF correction
8Coot0.9.5model fitting
9RELION3.1.3initial Euler assignment
10RELION3.1.3classification
11RELION3.1.33D reconstruction
12PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1215138
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213993 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418719
ELECTRON MICROSCOPYf_angle_d0.69825299
ELECTRON MICROSCOPYf_dihedral_angle_d15.0093281
ELECTRON MICROSCOPYf_chiral_restr0.0452532
ELECTRON MICROSCOPYf_plane_restr0.0053028

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