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- EMDB-14770: Late assembly intermediate of the proximal proton pumping module ... -

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Basic information

Entry
Database: EMDB / ID: EMD-14770
TitleLate assembly intermediate of the proximal proton pumping module of complex I with assembly factor NDUFAF1
Map datalate assembly intermediate of the proximal proton pumping module of complex I with assemble factor NDUFAF1
Sample
  • Complex: late Pp module assembly intermediate of complex I associated with assembly factor NDUFAF1.
Biological speciesYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSchiller J / Laube E / Vonck J / Zickermann V
Funding support Germany, 1 items
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, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14770.png

Downloads & links

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Map

FileDownload / File: emd_14770.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlate assembly intermediate of the proximal proton pumping module of complex I with assemble factor NDUFAF1
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 208 pix.
= 251.1 Å		1.21 Å/pix.
x 208 pix.
= 251.1 Å		1.21 Å/pix.
x 208 pix.
= 251.1 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.20721 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.0880017 - 1.9511836
Average (Standard dev.)0.0076054474 (±0.07921999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 251.09967 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14770_msk_1.map
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Additional map: map after density modification using Phenix

Fileemd_14770_additional_1.map
Annotationmap after density modification using Phenix
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Half map: #2

Fileemd_14770_half_map_1.map
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Half map: #1

Fileemd_14770_half_map_2.map
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Sample components

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Entire : late Pp module assembly intermediate of complex I associated with...

EntireName: late Pp module assembly intermediate of complex I associated with assembly factor NDUFAF1.
Components
  • Complex: late Pp module assembly intermediate of complex I associated with assembly factor NDUFAF1.

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Supramolecule #1: late Pp module assembly intermediate of complex I associated with...

SupramoleculeName: late Pp module assembly intermediate of complex I associated with assembly factor NDUFAF1.
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Yarrowia lipolytica (yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 276 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was a mixture of assembly intermediates associated with the assembly factor NDUFAF1

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6229 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2048808
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: OTHER / Details: Ab initio model in CryoSPARC 3.3.1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 20058
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7o71

RefinementSpace: REAL / Protocol: OTHER

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