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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
Sample
  • Complex: Rhesus 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

emd_0151.png

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)
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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Mask #1

Fileemd_0151_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_0151_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_0151_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 : Rhesus macaque mitochondrial complex I

EntireName: Rhesus macaque mitochondrial complex I
Components
  • Complex: Rhesus macaque mitochondrial complex I

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Supramolecule #1: Rhesus macaque mitochondrial complex I

SupramoleculeName: Rhesus macaque mitochondrial complex I / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca mulatta (Rhesus monkey) / Organ: Heart / Organelle: Mitochondria
Molecular weightTheoretical: 1 MDa

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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

Concentration3 mg/mL
BufferpH: 7.14
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chlorideSodium chloride
20.0 mMTris
0.05 %DDM
GridModel: Quantifoil, UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
Details: UltrAuFoil 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- ...Details: UltrAuFoil 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.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 8-16s blotting..
DetailsThe sample was collected from the peak fraction of a size-exclusion column and was not concentrated.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1) / Software - details: patch b1
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.1) / Software - details: patch b1
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1) / Software - details: patch b1
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Software - details: patch b1 / Number images used: 41688
FSC plot (resolution estimation)

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