[English] 日本語
Yorodumi
- PDB-8bep: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bep
TitleCryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)
Components
  • (Cytochrome b-c1 complex subunit ...) x 2
  • (Probable mitochondrial-processing peptidase subunit ...) x 2
KeywordsMEMBRANE PROTEIN / Plant / Mitochondria / Complex
Function / homology
Function and homology information


mitochondrial processing peptidase / plant-type cell wall / protein processing involved in protein targeting to mitochondrion / plant-type vacuole / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast ...mitochondrial processing peptidase / plant-type cell wall / protein processing involved in protein targeting to mitochondrion / plant-type vacuole / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial outer membrane / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / nucleolus / mitochondrion / proteolysis / zinc ion binding / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein ...Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit 7-2, mitochondrial / Probable mitochondrial-processing peptidase subunit beta, mitochondrial / Cytochrome b-c1 complex subunit Rieske-1, mitochondrial / Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 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 1.2Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
B: Probable mitochondrial-processing peptidase subunit beta, mitochondrial
D: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
F: Cytochrome b-c1 complex subunit 7-2, mitochondrial
K: Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
L: Probable mitochondrial-processing peptidase subunit beta, mitochondrial
N: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
P: Cytochrome b-c1 complex subunit 7-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,05110
Polymers315,9208
Non-polymers1312
Water16,105894
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area23040 Å2
ΔGint-168 kcal/mol
Surface area91810 Å2

-
Components

-
Probable mitochondrial-processing peptidase subunit ... , 2 types, 4 molecules AKBL

#1: Protein Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial / Alpha-MPP 1 / Complex III subunit II / Core protein II / Cytochrome b-c1 complex subunit 2-1 / ...Alpha-MPP 1 / Complex III subunit II / Core protein II / Cytochrome b-c1 complex subunit 2-1 / mitochondrial / Inactive zinc metalloprotease alpha-1 / Ubiquinol-cytochrome c oxidoreductase core protein 2-1


Mass: 54459.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZU25
#2: Protein Probable mitochondrial-processing peptidase subunit beta, mitochondrial / Beta-MPP / Complex III subunit I / Core protein I / Cytochrome b-c1 complex subunit 1 / ...Beta-MPP / Complex III subunit I / Core protein I / Cytochrome b-c1 complex subunit 1 / mitochondrial / Ubiquinol-cytochrome c oxidoreductase core protein 1


Mass: 59234.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q42290, mitochondrial processing peptidase

-
Cytochrome b-c1 complex subunit ... , 2 types, 4 molecules DNFP

#3: 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 7-2, mitochondrial / Complex III subunit 7-2 / Complex III subunit VII / Ubiquinol-cytochrome c oxidoreductase subunit 7-2


Mass: 14620.021 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4JWS8

-
Non-polymers , 2 types, 896 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 894 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)
Type: COMPLEX / Entity ID: #1-#4 / 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

-
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)

-
Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
5CTFFIND4.1.13CTF correction
8Coot0.9.5model fitting
9PHENIX1.20.1-4487model refinement
10RELION3.1.3initial Euler assignment
11RELION3.1.3classification
12RELION3.1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1215138
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213993 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00917054
ELECTRON MICROSCOPYf_angle_d0.8623123
ELECTRON MICROSCOPYf_dihedral_angle_d4.5862334
ELECTRON MICROSCOPYf_chiral_restr0.0422622
ELECTRON MICROSCOPYf_plane_restr0.0063013

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more