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Yorodumi- PDB-3j3y: Atomic-level structure of the entire HIV-1 capsid (186 hexamers +... -
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Basic information
| Entry | Database: PDB / ID: 3j3y | |||||||||
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| Title | Atomic-level structure of the entire HIV-1 capsid (186 hexamers + 12 pentamers) | |||||||||
 Components | capsid protein | |||||||||
 Keywords | VIRUS / HIV-1 capsid / core / all-atom model / complete capsid | |||||||||
| Function / homology |  Function and homology informationviral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding ...viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / identical protein binding / membrane 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. | |||||||||
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Structure visualization
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| Structure viewer | Molecule: MolmilJmol/JSmol |
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Downloads & links
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| PDBx/mmCIF format | 3j3y.cif.gz | 41.9 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb3j3y.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 3j3y.json.gz | Tree view | PDBx/mmJSON format | |
| Others |  Other downloads |
-Validation report
| Summary document | 3j3y_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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| Full document | 3j3y_full_validation.pdf.gz | 4.5 MB | Display | |
| Data in XML | 3j3y_validation.xml.gz | 2.9 MB | Display | |
| Data in CIF | 3j3y_validation.cif.gz | 6.5 MB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/3j3yftp://data.pdbj.org/pub/pdb/validation_reports/j3/3j3y | HTTPS FTP |
-Related structure data
| Related structure data |  5639MC  5582C  3j34C  3j3qC  3j4fC C: citing same article ( M: map data used to model this data |
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| Similar structure data |
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PDBj
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Assembly
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-Components
| #1: Protein | Mass: 25702.490 Da / Num. of mol.: 1176 / 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: Q79791Has protein modification | Y | |
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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 |
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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 |
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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 |
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Processing
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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 Accession code: 3J34 / Source name: PDB / Type: experimental model |
