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- EMDB-52664: Local refinement of complex IV (whole map) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52664
TitleLocal refinement of complex IV (whole map)
Map data
Sample
  • Cell: Respirasome complex map
KeywordsHuman mitochondria / respirasome complex / cytochrome c oxidase / complex IV / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNguyen MD / Rorbach J
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation023405053 Sweden
CitationJournal: To Be Published
Title: Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome
Authors: Nguyen MD / Khajawa A / Rorbach J
History
DepositionFeb 3, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52664.png

Downloads & links

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Map

FileDownload / File: emd_52664.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.245
Minimum - Maximum-1.0481548 - 2.1606379
Average (Standard dev.)-0.0054646046 (±0.043486908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 503.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52664_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52664_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Respirasome complex map

EntireName: Respirasome complex map
Components
  • Cell: Respirasome complex map

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Supramolecule #1: Respirasome complex map

SupramoleculeName: Respirasome complex map / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMKClpotassium chloride
25.0 mMC8H18N2O4SHepes
20.0 mMMg(CH3COO)2Magnesium acetate
0.01 %C47H88O22LMNG

Details: 25 mM HEPES-KOH pH=7.5, 50 mM KCl, 20 mM Mg(OAc)2, 0.01% (v/v) LMNG, 0.001 % cardiolipin, 0.001 % GD, 0.1mM DTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 17476 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xte

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 301780
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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