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- EMDB-5582: Cryo-EM structure of HIV-1 capsid assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-5582
TitleCryo-EM structure of HIV-1 capsid assembly
Map dataReal space helical reconstruction of HIV-1 capsid assembly
Sample
  • Sample: HIV-1 CA A92E
  • Protein or peptide: HIV-1 capsid protein
KeywordsHIV-1 capsid / core / tubular assembly / hexamer
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding ...viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / identical protein binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
Methodhelical reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsZhao G / Perilla JR / Yufenyuy E / Meng X / Chen B / Ning J / Ahn J / Gronenborn AM / Schulten K / Aiken C / Zhang P
CitationJournal: Nature / Year: 2013
Title: Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
Authors: Gongpu Zhao / Juan R Perilla / Ernest L Yufenyuy / Xin Meng / Bo Chen / Jiying Ning / Jinwoo Ahn / Angela M Gronenborn / Klaus Schulten / Christopher Aiken / Peijun Zhang /
Abstract: Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, ...Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.
History
DepositionFeb 12, 2013-
Header (metadata) releaseApr 3, 2013-
Map releaseMay 29, 2013-
UpdateJul 31, 2013-
Current statusJul 31, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 29
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 29
  • Imaged by UCSF Chimera
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  • Close-up
  • Surface view colored by cylindrical radius
  • Surface level: 29
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j34
  • Surface level: 29
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j4f
  • Surface level: 29
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j34
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j4f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5582_1.jpg

emd_5582_2.tif

Downloads & links

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Map

FileDownload / File: emd_5582.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReal space helical reconstruction of HIV-1 capsid assembly
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 664 pix.
= 723.76 Å		1.09 Å/pix.
x 664 pix.
= 723.76 Å		1.09 Å/pix.
x 664 pix.
= 723.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 29.0 / Movie #1: 29
Minimum - Maximum-25.537425989999999 - 62.554180150000001
Average (Standard dev.)-1.72483826 (±7.58703089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-332-332-332
Dimensions664664664
Spacing664664664
CellA=B=C: 723.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z664664664
origin x/y/z0.0000.0000.000
length x/y/z723.760723.760723.760
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-332-332-332
NC/NR/NS664664664
D min/max/mean-25.53762.554-1.725

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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 capsid protein

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Supramolecule #1000: HIV-1 CA A92E

SupramoleculeName: HIV-1 CA A92E / type: sample / ID: 1000 / Oligomeric state: helical assembly of hexamers / Number unique components: 6
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa

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Macromolecule #1: HIV-1 capsid protein

MacromoleculeName: HIV-1 capsid protein / type: protein_or_peptide / ID: 1 / Name.synonym: CA / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / synonym: HIV-1
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: Rosetta 2 (DE3) / Recombinant plasmid: pET21

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration2 mg/mL
BufferpH: 8 / Details: 1 M NaCl, 50 mM Tris-HCl
GridDetails: 200 mesh quantifoil R2/1 copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER
Method: With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side.

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 85 K / Average: 82 K
DateDec 11, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 27 / Average electron dose: 15 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58257 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe segments were aligned and reconstructed using Frealign. Twofold symmetry was imposed using IHRSR++.
Final reconstructionApplied symmetry - Helical parameters - Δz: 7.247 Å
Applied symmetry - Helical parameters - Δ&Phi: 31.13 °
Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Frealign
CTF correctionDetails: each filament

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Atomic model buiding 1

Initial modelPDB ID:

2kod

SoftwareName: MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j34:
Structure of HIV-1 Capsid Protein by Cryo-EM

PDB-3j4f:
Structure of HIV-1 capsid protein by cryo-EM

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Atomic model buiding 2

Initial modelPDB ID:

3h47

SoftwareName: MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j34:
Structure of HIV-1 Capsid Protein by Cryo-EM

PDB-3j4f:
Structure of HIV-1 capsid protein by cryo-EM

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