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Yorodumi- PDB-4arg: Structure of the immature retroviral capsid at 8A resolution by c... -
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-Basic information
Entry | Database: PDB / ID: 4arg | ||||||
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Title | Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy | ||||||
Components | (M-PMV DPRO CANC PROTEIN) x 2 | ||||||
Keywords | VIRAL PROTEIN / RETROVIRUS | ||||||
Function / homology | Retroviral 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 species | MASON-PFIZER MONKEY VIRUS | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D | ||||||
Authors | Bharat, T.A.M. / Davey, N.E. / Ulbrich, P. / Riches, J.D. / Marco, A.D. / Rumlova, M. / Sachse, C. / Ruml, T. / Briggs, J.A.G. | ||||||
Citation | Journal: 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 |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 4arg.cif.gz | 23.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4arg.ent.gz | 10.7 KB | Display | PDB format |
PDBx/mmJSON format | 4arg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4arg_validation.pdf.gz | 830.2 KB | Display | wwPDB validaton report |
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Full document | 4arg_full_validation.pdf.gz | 831.8 KB | Display | |
Data in XML | 4arg_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 4arg_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/4arg ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4arg | HTTPS FTP |
-Related structure data
Related structure data | 2089MC 2090MC 4ardC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 | 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 details | THIS 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 CYCLOPHILI | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: M-PMV CANC GAG TUBES / Type: COMPLEX |
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Buffer solution | Name: 100MM NACL, 50MM TRIS-HCL, 1UM ZN / pH: 7.7 / Details: 100MM NACL, 50MM TRIS-HCL, 1UM ZN |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jul 5, 2011 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 0.2 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 46 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: DIVISION BY 3D CTF SQ | |||||||||||||||||||||
3D reconstruction | Method: 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 building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--NMR,XRAY | |||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 7 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7 Å
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