+Open data
-Basic information
Entry | Database: PDB / ID: 3j3q | |||||||||
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Title | Atomic-level structure of the entire HIV-1 capsid | |||||||||
Components | capsid protein | |||||||||
Keywords | VIRUS / HIV-1 capsid / core / all-atom model / complete capsid | |||||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM | |||||||||
Authors | Perilla, J.R. / Zhao, G. / Zhang, P. / Schulten, K.J. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j3q.cif.gz | 47.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3j3q.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 3j3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j3q_validation.pdf.gz | 9.6 MB | Display | wwPDB validaton report |
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Full document | 3j3q_full_validation.pdf.gz | 17.6 MB | Display | |
Data in XML | 3j3q_validation.xml.gz | 3.6 MB | Display | |
Data in CIF | 3j3q_validation.cif.gz | 6.9 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/3j3q ftp://data.pdbj.org/pub/pdb/validation_reports/j3/3j3q | HTTPS FTP |
-Related structure data
Related structure data | 5639MC 5582C 3j34C 3j3yC 3j4fC 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: 25702.490 Da / Num. of mol.: 1356 / Fragment: UNP residues 133-363 / Mutation: A92E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q79791 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: electron tomography |
-Sample preparation
Component | Name: HIV-1 core with A14C/E45C cross-linked capsid protein / Type: VIRUS |
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Details of virus | Empty: NO / Enveloped: YES / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | Name: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA / pH: 8 / Details: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA |
Specimen | Conc.: 0.011 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Quantifoil R2/2 200 mesh holey carbon copper grids |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Sep 11, 2010 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Nominal defocus max: 8000 nm / Nominal defocus min: 8000 nm / Cs: 2 mm |
Specimen holder | Specimen holder model: SIDE ENTRY, EUCENTRIC / Temperature: 82 K / Temperature (max): 85 K / Temperature (min): 80 K / Tilt angle max: 66 ° / Tilt angle min: -70 ° |
Image recording | Electron dose: 120 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 53 |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||
3D reconstruction | Method: SIRT / Nominal pixel size: 6.25 Å / Actual pixel size: 6.25 Å / Symmetry type: POINT | |||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: REFINEMENT PROTOCOL--FLEXIBLE DETAILS--The model was built using hexamer of hexamers (PDB entry 3J34) and pentamer of hexamers (computer-based MD model available upon request). | |||||||||
Atomic model building | PDB-ID: 3J34 |