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- PDB-4arg: Structure of the immature retroviral capsid at 8A resolution by c... -

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Entry
Database: PDB / ID: 4arg
TitleStructure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy
Components(M-PMV DPRO CANC PROTEIN) x 2
KeywordsVIRAL PROTEIN / RETROVIRUS
Function / homologyRetroviral nucleocapsid Gag protein p24, N-terminal / virion component => GO:0044423 / gag protein p24 N-terminal domain / viral process / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / M-pmv dpro canc protein / M-pmv dpro canc protein
Function and homology information
Biological speciesMASON-PFIZER MONKEY VIRUS
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D
AuthorsBharat, T.A.M. / Davey, N.E. / Ulbrich, P. / Riches, J.D. / Marco, A.D. / Rumlova, M. / Sachse, C. / Ruml, T. / Briggs, J.A.G.
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, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id

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Assembly

Deposited unit
A: M-PMV DPRO CANC PROTEIN
B: M-PMV DPRO CANC PROTEIN
C: M-PMV DPRO CANC PROTEIN
D: M-PMV DPRO CANC PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,2194
Polymers44,2194
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein M-PMV DPRO CANC PROTEIN / Coordinate model: Cα atoms only


Mass: 14371.477 Da / Num. of mol.: 2 / Fragment: M-PMV CA-NTD DIMER, RESIDUES 149-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MASON-PFIZER MONKEY VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: I6L8L3*PLUS
#2: Protein M-PMV DPRO CANC PROTEIN / Coordinate model: Cα atoms only


Mass: 7737.796 Da / Num. of mol.: 2 / Fragment: M-PMV CA-NTD DIMER, RESIDUES 283-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MASON-PFIZER MONKEY VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: I6L8L4*PLUS
Sequence detailsTHIS ENTRY FITS THE STRUCTURE OF HIV (UNP Q72497) INTO THE ELCTRON DENSITY MAP OF MPMV (EM 2089). ...THIS ENTRY FITS THE STRUCTURE OF HIV (UNP Q72497) INTO THE ELCTRON DENSITY MAP OF MPMV (EM 2089). THE CYCLOPHILIN BINDING LOOP OF HIV-1 (PVHAGPIAPGQMREP) AND THE SEQUENCE OF RESIDUES (SPTSI) IN THE INTER-DOMAIN LINKER WERE NOT INCLUDED FOR THE FITTING.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: M-PMV CANC GAG TUBES / Type: COMPLEX
Buffer solutionName: 100MM NACL, 50MM TRIS-HCL, 1UM ZN / pH: 7.7 / Details: 100MM NACL, 50MM TRIS-HCL, 1UM ZN
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 5, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 0.2 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 46
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2AV33D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: DIVISION BY 3D CTF SQ
3D reconstructionMethod: REAL SPACE HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING.
Resolution: 7 Å / Nominal pixel size: 1.53 Å / Actual pixel size: 1.53 Å
Details: REAL SPACE HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2089. (DEPOSITION ID: 10767).
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--NMR,XRAY
Atomic model building
IDPDB-ID 3D fitting-ID
11L6N1
22KGF1
RefinementHighest resolution: 7 Å
Refinement stepCycle: LAST / Highest resolution: 7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms366 0 0 0 366

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