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- EMDB-5136: CryoEM Structure of Tubular Assembly of HIV-1 CA and Evidence for... -

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Basic information

Database: EMDB / ID: 5136
TitleCryoEM Structure of Tubular Assembly of HIV-1 CA and Evidence for a Novel Interface
Map dataThis is a map of tubular assembly of HIV-1 CA
SampleHIV-1 CA A92E:
HIV-1 CA protein
SourceHuman immunodeficiency virus (Human immunodeficiency virus)
Methodhelical reconstruction / cryo EM / 16 Å resolution
AuthorsByeon IL / Meng X / Jung J / Zhao G / Ahn J / Concel J / Aiken C / Gronenborn AM / Zhang P
CitationJournal: Cell / Year: 2009
Title: Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
Authors: In-Ja L Byeon / Xin Meng / Jinwon Jung / Gongpu Zhao / Ruifeng Yang / Jinwoo Ahn / Jiong Shi / Jason Concel / Christopher Aiken / Peijun Zhang / Angela M Gronenborn
DateDeposition: Oct 20, 2009 / Header (metadata) release: Nov 9, 2009 / Map release: May 5, 2010 / Last update: Sep 27, 2011

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_5136.map.gz (map file in CCP4 format, 27001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
2.15 Å/pix.
= 258. Å
240 pix
2.15 Å/pix.
= 516. Å
240 pix
2.15 Å/pix.
= 516. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.15 Å
Contour Level:0.01 (by emdb), 0.0055 (movie #1):
Minimum - Maximum-0.0263844 - 0.0278307
Average (Standard dev.)0.00019507 (0.00626063)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 516 Å / B: 516 Å / C: 258 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.152.152.15
M x/y/z240240120
origin x/y/z0.0000.0000.000
length x/y/z516.000516.000258.000
start NX/NY/NZ-34-26-72
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0260.0280.000

Supplemental data

Sample components

Entire HIV-1 CA A92E

EntireName: HIV-1 CA A92E / Details: component name, HIV-1 CA protein / Number of components: 6

Component #1: protein, HIV-1 CA protein

ProteinName: HIV-1 CA protein / a.k.a: hexamerOligomer / Recombinant expression: Yes
SourceSpecies: Human immunodeficiency virus (Human immunodeficiency virus)

Experimental details

Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersHand: RIGHT HANDED
VitrificationInstrument: NONE / Cryogen name: NITROGEN

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: liquid nitrogen-cooled cryo specimen holder / Model: GATAN LIQUID NITROGEN

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 16 Å / Resolution method: FSC 0.5

Atomic model buiding

Modeling #1Software: Chimera / Refinement space: REAL
Input PDB model: 3DIK

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