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- EMDB-2090: Structure of the immature retroviral capsid at 8A resolution by c... -

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Basic information

Entry
Database: EMDB / ID: EMD-2090
TitleStructure of the immature retroviral capsid at 8A resolution by cryo-electron microscopy
Map dataReconstruction of the M-PMV CANC Gag dimer
Sample
  • Sample: M-PMV CANC Gag dimer
  • Protein or peptide: M-PMV dPro CANC protein
Keywordsretrovirus / capsid / gag
Function / homology
Function and homology information


virion component => GO:0044423 / viral budding via host ESCRT complex / viral process / viral nucleocapsid / host cell cytoplasm / structural constituent of virion / nucleic acid binding / zinc ion binding / metal ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / 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 finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
M-pmv dpro canc protein / M-pmv dpro canc protein / Gag polyprotein
Similarity search - Component
Biological speciesMason-Pfizer monkey virus
Methodhelical reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsBharat TAM / Davey NE / Ulbrich P / Riches JD / de Marco A / Rumlova M / Sachse C / Ruml T / Briggs JAG
CitationJournal: Nature / Year: 2012
Title: Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy.
Authors: Tanmay A M Bharat / Norman E Davey / Pavel Ulbrich / James D Riches / Alex de Marco / Michaela Rumlova / Carsten Sachse / Tomas Ruml / John A G Briggs /
Abstract: The assembly of retroviruses such as HIV-1 is driven by oligomerization of their major structural protein, Gag. Gag is a multidomain polyprotein including three conserved folded domains: MA (matrix), ...The assembly of retroviruses such as HIV-1 is driven by oligomerization of their major structural protein, Gag. Gag is a multidomain polyprotein including three conserved folded domains: MA (matrix), CA (capsid) and NC (nucleocapsid). Assembly of an infectious virion proceeds in two stages. In the first stage, Gag oligomerization into a hexameric protein lattice leads to the formation of an incomplete, roughly spherical protein shell that buds through the plasma membrane of the infected cell to release an enveloped immature virus particle. In the second stage, cleavage of Gag by the viral protease leads to rearrangement of the particle interior, converting the non-infectious immature virus particle into a mature infectious virion. The immature Gag shell acts as the pivotal intermediate in assembly and is a potential target for anti-retroviral drugs both in inhibiting virus assembly and in disrupting virus maturation. However, detailed structural information on the immature Gag shell has not previously been available. For this reason it is unclear what protein conformations and interfaces mediate the interactions between domains and therefore the assembly of retrovirus particles, and what structural transitions are associated with retrovirus maturation. Here we solve the structure of the immature retroviral Gag shell from Mason-Pfizer monkey virus by combining cryo-electron microscopy and tomography. The 8-Å resolution structure permits the derivation of a pseudo-atomic model of CA in the immature retrovirus, which defines the protein interfaces mediating retrovirus assembly. We show that transition of an immature retrovirus into its mature infectious form involves marked rotations and translations of CA domains, that the roles of the amino-terminal and carboxy-terminal domains of CA in assembling the immature and mature hexameric lattices are exchanged, and that the CA interactions that stabilize the immature and mature viruses are almost completely distinct.
History
DepositionApr 23, 2012-
Header (metadata) releaseMay 17, 2012-
Map releaseMay 25, 2012-
UpdateJul 25, 2012-
Current statusJul 25, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4ard
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4arg
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4ard
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4arg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2090.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the M-PMV CANC Gag dimer
Voxel sizeX=Y=Z: 1.53 Å
Density
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.42414615 - 0.51569301
Average (Standard dev.)0.01457752 (±0.16203351)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 91.799995 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.531.531.53
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z91.80091.80091.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean-0.4240.5160.015

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Supplemental data

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Sample components

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Entire : M-PMV CANC Gag dimer

EntireName: M-PMV CANC Gag dimer
Components
  • Sample: M-PMV CANC Gag dimer
  • Protein or peptide: M-PMV dPro CANC protein

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Supramolecule #1000: M-PMV CANC Gag dimer

SupramoleculeName: M-PMV CANC Gag dimer / type: sample / ID: 1000 / Oligomeric state: Helical / Number unique components: 1

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Macromolecule #1: M-PMV dPro CANC protein

MacromoleculeName: M-PMV dPro CANC protein / type: protein_or_peptide / ID: 1 / Oligomeric state: Helical / Recombinant expression: Yes
Source (natural)Organism: Mason-Pfizer monkey virus
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.7 / Details: 50mM Tris, 100mM NaCl, 1uM Zn
GridDetails: 300 mesh copper, glow discharged
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 47000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateApr 23, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 46 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Division by 3D CTF^2
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: OTHER / Software - Name: Spider, AV3
DetailsReconstruction carried out using real-space helical reconstruction followed by 3D averaging of the asymmetric unit from assemblies with different helical symmetry parameters.

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Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: UCSF Chimera
DetailsProtocol: Rigid body. Two copies of the M-PMV CA-NTD domain were fitted separately.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4ard:
Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy

PDB-4arg:
Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy

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Atomic model buiding 2

Initial modelPDB ID:
SoftwareName: UCSF Chimera
DetailsProtocol: Rigid body. Two copies of the CA-NTD domain were fitted separately.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4ard:
Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy

PDB-4arg:
Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy

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Atomic model buiding 3

Initial modelPDB ID:

Chain - Chain ID: L
SoftwareName: UCSF Chimera
DetailsProtocol: Rigid body. Two copies of the CA-CTD domains were fitted separately.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4ard:
Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy

PDB-4arg:
Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy

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