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

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Entry
Database: PDB / ID: 4ard
TitleStructure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy
ComponentsCAPSID PROTEIN P27
KeywordsVIRAL PROTEIN / RETROVIRUS / GAG
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / nucleic acid binding / structural constituent of virion / viral translational frameshifting / zinc ion binding / metal ion binding
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / 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 ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / 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
Biological speciesMASON-PFIZER MONKEY VIRUS
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B
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 1.2Apr 19, 2017Group: Other
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4Apr 24, 2019Group: Data collection / Other
Category: atom_sites / cell ...atom_sites / cell / database_PDB_rev / database_PDB_rev_record
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma
Revision 1.5May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: CAPSID PROTEIN P27
B: CAPSID PROTEIN P27


Theoretical massNumber of molelcules
Total (without water)25,7702
Polymers25,7702
Non-polymers00
Water00
1


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

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Components

#1: Protein CAPSID PROTEIN P27 / M-PMV DPRO CANC PROTEIN / Coordinate model: Cα atoms only


Mass: 12885.230 Da / Num. of mol.: 2 / Fragment: M-PMV CA-NTD, RESIDUES 318-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MASON-PFIZER MONKEY VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07567

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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 FIELD / 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: HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING
Resolution: 7 Å / Nominal pixel size: 1.53 Å / Actual pixel size: 1.53 Å
Details: HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2090. (DEPOSITION ID: 10768).
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--NMR
Atomic model buildingPDB-ID: 2KGF

2kgf


Accession code: 2KGF / Source name: PDB / Type: experimental model
RefinementHighest resolution: 7 Å
Refinement stepCycle: LAST / Highest resolution: 7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms232 0 0 0 232

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