+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-0151 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Rhesus macaque mitochondrial complex I | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Agip ANA / Blaza JN / Fedor JG / Hirst J | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 167 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 15.9 KB 15.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 39.3 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Others | ![]() ![]() | 140.7 MB 141 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_0151_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_0151_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Rhesus macaque mitochondrial complex I
Entire | Name: Rhesus macaque mitochondrial complex I |
---|---|
Components |
|
-Supramolecule #1: Rhesus macaque mitochondrial complex I
Supramolecule | Name: Rhesus macaque mitochondrial complex I / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 3 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.14 Component:
| ||||||||||||
Grid | Model: 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. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 8-16s blotting.. | ||||||||||||
Details | The sample was collected from the peak fraction of a size-exclusion column and was not concentrated. |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |