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- PDB-7zkp: Late assembly intermediate of the proximal proton pumping module ... -

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Basic information

Entry
Database: PDB / ID: 7zkp
TitleLate assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84
Components
  • (NADH-ubiquinone oxidoreductase chain ...) x 4
  • CIA30 domain-containing protein
  • NADH dehydrogenase subunit 2
  • NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein
  • Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • assembly factor CIA84
  • subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
KeywordsELECTRON TRANSPORT / assembly respiratory chain membrane protein mitochondria
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / mitochondrial membrane / mitochondrial intermembrane space / mitochondrial inner membrane / oxidoreductase activity ...NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / mitochondrial membrane / mitochondrial intermembrane space / mitochondrial inner membrane / oxidoreductase activity / mitochondrion / membrane
Similarity search - Function
NADH:ubiquinone oxidoreductase intermediate-associated protein 30 / Complex I intermediate-associated protein 30, mitochondrial / Complex I intermediate-associated protein 30 (CIA30) / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit ...NADH:ubiquinone oxidoreductase intermediate-associated protein 30 / Complex I intermediate-associated protein 30, mitochondrial / Complex I intermediate-associated protein 30 (CIA30) / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / GRIM-19 / GRIM-19 protein / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / CHCH domain / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-CPL / DIUNDECYL PHOSPHATIDYL CHOLINE / Phosphatidylinositol / Complex I intermediate-associated protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / CIA30 domain-containing protein / Uncharacterized protein / Uncharacterized protein ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-CPL / DIUNDECYL PHOSPHATIDYL CHOLINE / Phosphatidylinositol / Complex I intermediate-associated protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / CIA30 domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH-ubiquinone oxidoreductase / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 4L
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
L: NADH-ubiquinone oxidoreductase chain 4L
U: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
W: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
X: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein
1: NADH-ubiquinone oxidoreductase chain 1
2: NADH dehydrogenase subunit 2
3: NADH-ubiquinone oxidoreductase chain 3
6: NADH-ubiquinone oxidoreductase chain 6
g: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
b: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
9: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
C: assembly factor CIA84
A: CIA30 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,53620
Polymers355,59214
Non-polymers5,9446
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area78980 Å2
ΔGint-636 kcal/mol
Surface area93420 Å2
MethodPISA

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Components

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Protein , 10 types, 10 molecules DUWX2gb9CA

#1: Protein Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9806.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NC63
#3: Protein Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19355.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C2D0
#4: Protein Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14112.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PPE5
#5: Protein NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein


Mass: 18588.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NKB4
#7: 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)
#10: Protein subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8992.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NJR0
#11: 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
#12: Protein Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10035.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NNZ0
#13: Protein 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
#14: Protein CIA30 domain-containing protein


Mass: 32629.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NDUFAF1 has a C-terminal strep tag / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_D17795g / Production host: Yarrowia lipolytica (yeast) / Variant (production host): deletion of NDUFAF1 / References: UniProt: A0A1D8NEL0

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NADH-ubiquinone oxidoreductase chain ... , 4 types, 4 molecules L136

#2: Protein NADH-ubiquinone oxidoreductase chain 4L


Mass: 9843.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U4U1, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 38389.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U3V2, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NADH-ubiquinone oxidoreductase chain 3


Mass: 14506.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TMS4, NADH:ubiquinone reductase (H+-translocating)
#9: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 20793.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U3X7, NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 5 types, 6 molecules

#15: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#16: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#17: Chemical ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 758.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
#18: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#19: Chemical ChemComp-T7X / Phosphatidylinositol / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H83O13P

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Details

Has ligand of interestN

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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: Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84
Type: COMPLEX / Entity ID: #1-#14 / 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 mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 276 K

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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 FIELDBright-field microscopy / 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

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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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18279 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 7O71

7o71

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