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- EMDB-8986: A 3.1 Angstrom sub-tomogram average of HIV-1 CA-SP1. -

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Basic information

Database: EMDB / ID: 8986
TitleA 3.1 Angstrom sub-tomogram average of HIV-1 CA-SP1.
Map dataMap with a B-factor of 150 applied, as used in generating figures.
SampleHIV-1 CA-SP1:
Methodsubtomogram averaging / cryo EM / 3.1 Å resolution
AuthorsHimes BA / Zhang P
CitationJournal: Nat. Methods / Year: 2018
Title: emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging.
Authors: Benjamin A Himes / Peijun Zhang
DateDeposition: Jul 22, 2018 / Header (metadata) release: Oct 31, 2018 / Map release: Oct 31, 2018 / Last update: Nov 21, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.993267486
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_8986.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1 Å/pix.
= 256. Å
256 pix
1 Å/pix.
= 256. Å
256 pix
1 Å/pix.
= 256. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Contour Level:2.4 (by author), 0.9932675 (movie #1):
Minimum - Maximum-8.348758999999999 - 14.062434
Average (Standard dev.)0.013832731 (0.6134586)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 256.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-8.34914.0620.014

Supplemental data

Sample components

Entire HIV-1 CA-SP1

EntireName: HIV-1 CA-SP1 / Number of components: 1

Component #1: virus, HIV-1 CA-SP1

VirusName: HIV-1 CA-SP1 / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: OTHER

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Please refer to EMD-3782/ EMPIAR-10164
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3.4 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

Image acquisition

Image acquisitionDetails: Please refer to EMD-3782/ EMPIAR-10164

Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C6 (6 fold cyclic) / Number of subtomograms: 162215 / Number of class averages: 1 / Details: Please refer to EMD-3782/ EMPIAR-10164
3D reconstructionAlgorithm: BACK PROJECTION
CTF correction: "3D-CTF" (defocus gradient corrected back-projection) using emClarity 1.0.0
Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Details: using emClarity 1.0.0 / Euler angles: Missing wedge compensated cross-correlation.
FSC plot
(resolution estimation)

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