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

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Basic information

Entry
Database: EMDB / ID: EMD-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
Sample
  • Sample: HIV-1 CA A92E
  • Protein or peptide: HIV-1 CA protein
Biological speciesHuman immunodeficiency virus
Methodhelical reconstruction / cryo EM / Resolution: 16.0 Å
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 /
Abstract: Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three- ...Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three-dimensional arrays of the capsid protein (CA) hexamer revealed three interfaces. Here, we present a cryoEM study of a tubular assembly of CA and a high-resolution NMR structure of the CA C-terminal domain (CTD) dimer. In the solution dimer structure, the monomers exhibit different relative orientations compared to previous X-ray structures. The solution structure fits well into the EM density map, suggesting that the dimer interface is retained in the assembled CA. We also identified a CTD-CTD interface at the local three-fold axis in the cryoEM map and confirmed its functional importance by mutagenesis. In the tubular assembly, CA intermolecular interfaces vary slightly, accommodating the asymmetry present in tubes. This provides the necessary plasticity to allow for controlled virus capsid dis/assembly.
History
DepositionOct 20, 2009-
Header (metadata) releaseNov 9, 2009-
Map releaseMay 5, 2010-
UpdateSep 27, 2011-
Current statusSep 27, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • 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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5136_1.tif

Downloads & links

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Map

FileDownload / File: emd_5136.map.gz / Format: CCP4 / Size: 25.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of tubular assembly of HIV-1 CA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.15 Å/pix.
x 120 pix.
= 258. Å		2.15 Å/pix.
x 240 pix.
= 516. Å		2.15 Å/pix.
x 240 pix.
= 516. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.01 / Movie #1: 0.0055
Minimum - Maximum-0.0263844 - 0.0278307
Average (Standard dev.)0.00019507 (±0.00626063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240120
Spacing240240120
CellA: 516 Å / B: 516 Å / C: 258 Å
α=β=γ: 90 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240120
D min/max/mean-0.0260.0280.000

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Supplemental data

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Sample components

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Entire : HIV-1 CA A92E

EntireName: HIV-1 CA A92E
Components
  • Sample: HIV-1 CA A92E
  • Protein or peptide: HIV-1 CA protein

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Supramolecule #1000: HIV-1 CA A92E

SupramoleculeName: HIV-1 CA A92E / type: sample / ID: 1000 / Details: component name, HIV-1 CA protein / Number unique components: 6

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Macromolecule #1: HIV-1 CA protein

MacromoleculeName: HIV-1 CA protein / type: protein_or_peptide / ID: 1 / Name.synonym: hexamer / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Human immunodeficiency virus / synonym: Human immunodeficiency virus

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding 1

Initial modelPDB ID:

3dik

SoftwareName: Chimera
RefinementSpace: REAL

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