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- EMDB-0151: Rhesus macaque mitochondrial complex I -

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Basic information

Entry
Database: EMDB / ID: EMD-0151
TitleRhesus macaque mitochondrial complex I
Map data
SampleRhesus macaque mitochondrial complex I
Biological speciesMacaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsAgip ANA / Blaza JN / Fedor JG / Hirst J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105663141 United Kingdom
CitationJournal: Annu Rev Biophys / Year: 2019
Title: Mammalian Respiratory Complex I Through the Lens of Cryo-EM.
Authors: Ahmed-Noor A Agip / James N Blaza / Justin G Fedor / Judy Hirst /
Abstract: Single-particle electron cryomicroscopy (cryo-EM) has led to a revolution in structural work on mammalian respiratory complex I. Complex I (mitochondrial NADH:ubiquinone oxidoreductase), a membrane- ...Single-particle electron cryomicroscopy (cryo-EM) has led to a revolution in structural work on mammalian respiratory complex I. Complex I (mitochondrial NADH:ubiquinone oxidoreductase), a membrane-bound redox-driven proton pump, is one of the largest and most complicated enzymes in the mammalian cell. Rapid progress, following the first 5-Å resolution data on bovine complex I in 2014, has led to a model for mouse complex I at 3.3-Å resolution that contains 96% of the 8,518 residues and to the identification of different particle classes, some of which are assigned to biochemically defined states. Factors that helped improve resolution, including improvements to biochemistry, cryo-EM grid preparation, data collection strategy, and image processing, are discussed. Together with recent structural data from an ancient relative, membrane-bound hydrogenase, cryo-EM on mammalian complex I has provided new insights into the proton-pumping machinery and a foundation for understanding the enzyme's catalytic mechanism.
History
DepositionJul 30, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseJul 31, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0151.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 360 pix.
= 500.4 Å
1.39 Å/pix.
x 360 pix.
= 500.4 Å
1.39 Å/pix.
x 360 pix.
= 500.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.49333614 - 1.4516327
Average (Standard dev.)0.0000578142 (±0.026185205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 500.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z500.400500.400500.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.4931.4520.000

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Supplemental data

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Segmentation: #1

Fileemd_0151_msk_1.map
Projections & Slices
AxesZYX

Projections

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Density Histograms

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Half map: #1

Fileemd_0151_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_0151_half_map_2.map
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Sample components

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Entire Rhesus macaque mitochondrial complex I

EntireName: Rhesus macaque mitochondrial complex I / Number of Components: 1

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Component #1: protein, Rhesus macaque mitochondrial complex I

ProteinName: Rhesus macaque mitochondrial complex I / Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Macaca mulatta (Rhesus monkey)
Source (natural)Organelle: Mitochondria / Organ Or Tissue: Heart

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/mL / pH: 7.14
Support filmUltrAuFoil gold grids (0.6/1) was used for the preparation of macaque complex I grids. In brief, UltrAuFoil gold grids (0.6/1) were glow discharged at 20 mA for 60 sec using a EMITECH glow-discharger unit. Then, the grids were incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol (SPT-0011P6, SensoPath Technologies) in ethanol for two days under anaerobic conditions.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: 8-16s blotting..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 50 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 41688
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 4.1 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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