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- EMDB-9203: bovine glutamate dehydrogenase (18apr21a) -

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Basic information

Entry
Database: EMDB / ID: 9203
Titlebovine glutamate dehydrogenase (18apr21a)
Map databovine glutamate dehydrogenase map (18apr21a)
Samplebovine liver glutamate dehydrogenase:
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 2.1 Å resolution
AuthorsEng ET / Kopylov M / Negro CJ / Dallaykan S / Jordan KJ / Kelley K / Rice WJ / Carragher BO / Potter CS
CitationJournal: To Be Published
Title: bovine glutamate dehydrogenase (18apr21a)
Authors: Eng ET / Kopylov M / Negro CJ / Dallaykan S / Jordan KJ / Kelley K / Rice WJ / Carragher BO / Potter CS
DateDeposition: Oct 13, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Oct 24, 2018 / Last update: Oct 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9203.map.gz (map file in CCP4 format, 174457 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
352 pix
0.66 Å/pix.
= 232.883 Å
352 pix
0.66 Å/pix.
= 232.883 Å
352 pix
0.66 Å/pix.
= 232.883 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6616 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.07137104 - 0.14005539
Average (Standard dev.)0.00017214128 (0.0037602698)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions352352352
Origin0.00.00.0
Limit351.0351.0351.0
Spacing352352352
CellA=B=C: 232.8832 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.661599431818180.661599431818180.66159943181818
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z232.883232.883232.883
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0710.1400.000

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Supplemental data

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Mask #1

Fileemd_9203_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire bovine liver glutamate dehydrogenase

EntireName: bovine liver glutamate dehydrogenase / Number of components: 1

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Component #1: protein, bovine liver glutamate dehydrogenase

ProteinName: bovine liver glutamate dehydrogenase / Recombinant expression: No
MassTheoretical: 347 kDa
SourceSpecies: Bos taurus (cattle)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/ml / pH: 7.4
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 75 % / Details: Blotted for 2.5 s after a 30 s wait time.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Leginon
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 61.25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37000.0 X (nominal), 75574.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 70.0 - 70.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2491 / Sampling size: 5 microns
Details: Images were collected in movie mode at 10 frames per second.
Raw dataEMPIAR-10217 (Title: bovine liver glutamate dehydrogenase / Data size: 264.5
Data #1: aligned micrographs of bovine liver glutamate dehydrogenase (18apr21a) [micrographs - single frame])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D3 (2*3 fold dihedral) / Number of projections: 285518
Details: Images were automatically run through MotionCor2 by Appion on-the-fly with the aligned sum and aligned dose-weighted sum saved.
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION
CTF correction: CTF amplitude correction was performed following 3D reconstruction.
Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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