[English] 日本語
Yorodumi
- PDB-7zkq: Early Pp module assembly intermediate of complex I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zkq
TitleEarly Pp module assembly intermediate of complex I
Components
  • Complex I intermediate-associated protein 30-domain-containing protein
  • NADH dehydrogenase subunit 2
  • Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Tafazzin family protein
  • complex I assembly factor CIA84
KeywordsELECTRON TRANSPORT / assembly respiratory chain membrane protein mitochondria
Function / homology
Function and homology information


NADH dehydrogenase complex assembly / cardiolipin acyl-chain remodeling / 1-acylglycerophosphocholine O-acyltransferase activity / inner mitochondrial membrane organization / mitochondrial respirasome assembly / phospholipid biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial membrane ...NADH dehydrogenase complex assembly / cardiolipin acyl-chain remodeling / 1-acylglycerophosphocholine O-acyltransferase activity / inner mitochondrial membrane organization / mitochondrial respirasome assembly / phospholipid biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial membrane / unfolded protein binding / mitochondrial outer membrane / oxidoreductase activity / mitochondrial inner membrane / mitochondrion / membrane
Similarity search - Function
Tafazzin / NADH:ubiquinone oxidoreductase intermediate-associated protein 30 / Complex I intermediate-associated protein 30, mitochondrial / Complex I intermediate-associated protein 30 (CIA30) / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases / Galactose-binding lectin / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM ...Tafazzin / NADH:ubiquinone oxidoreductase intermediate-associated protein 30 / Complex I intermediate-associated protein 30, mitochondrial / Complex I intermediate-associated protein 30 (CIA30) / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases / Galactose-binding lectin / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CARDIOLIPIN / DIUNDECYL PHOSPHATIDYL CHOLINE / Mitochondrial group I intron splicing factor CCM1 / Uncharacterized protein / Complex I intermediate-associated protein 30-domain-containing protein / Tafazzin family protein / NADH-ubiquinone oxidoreductase chain 2
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsSchiller, J. / Laube, E. / Vonck, J. / Zickermann, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)ZI 552/4-2 Germany
CitationJournal: Sci Adv / Year: 2022
Title: Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling.
Authors: Jonathan Schiller / Eike Laube / Ilka Wittig / Werner Kühlbrandt / Janet Vonck / Volker Zickermann /
Abstract: Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly ...Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system. Subunits ND2 and NDUFC2 together with assembly factors NDUFAF1 and CIA84 form the nucleation point of the NDUFAF1-dependent assembly pathway. Unexpectedly, the cardiolipin remodeling enzyme tafazzin is an integral component of this core complex. In a later intermediate, all 12 subunits of the proximal proton pump module have assembled. NDUFAF1 locks the central ND3 subunit in an assembly-competent conformation, and major rearrangements of central subunits are required for complex I maturation.
History
DepositionApr 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_initial_refinement_model / struct
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _struct.title
Revision 1.2Nov 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_modification_feature
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
2: NADH dehydrogenase subunit 2
b: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
A: Complex I intermediate-associated protein 30-domain-containing protein
C: complex I assembly factor CIA84
T: Tafazzin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,8259
Polymers233,2695
Non-polymers4,5564
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17350 Å2
ΔGint-83 kcal/mol
Surface area63920 Å2
MethodPISA

-
Components

-
Protein , 5 types, 5 molecules 2bACT

#1: Protein NADH dehydrogenase subunit 2


Mass: 53381.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U4R9, NADH:ubiquinone reductase (H+-translocating)
#2: Protein Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8059.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NGI5
#3: Protein Complex I intermediate-associated protein 30-domain-containing protein


Mass: 31894.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal strep tag / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_38716 / Production host: Yarrowia lipolytica (yeast) / Variant (production host): deletion of NDUFAF1 / References: UniProt: A0A371C5R6
#4: Protein complex I assembly factor CIA84


Mass: 97098.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N612
#5: Protein Tafazzin family protein


Mass: 42835.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150 / References: UniProt: Q6CBZ7

-
Non-polymers , 3 types, 4 molecules

#6: 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.: 2 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#7: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#8: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Early Pp module assembly intermediate of complex I with assembly factors NDUFAF1 and CIA84 and cardiolipin remodeling enzyme tafazzin.
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Buffer solutionpH: 7.5
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was a mixture of assembly intermediates associated with the assembly factor NDUFAF1
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 276 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6229

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9model fitting
9PHENIXmodel refinement
10cryoSPARC3.3.1initial Euler assignment
11cryoSPARC3.3.1final Euler assignment
13cryoSPARC3.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2048808
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 376810 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 7O71

7o71


Accession code: 7O71 / Source name: PDB / Type: experimental model

+
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://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