+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5582 | |||||||||
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Title | Cryo-EM structure of HIV-1 capsid assembly | |||||||||
Map data | Real space helical reconstruction of HIV-1 capsid assembly | |||||||||
Sample |
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Keywords | HIV-1 capsid / core / tubular assembly / hexamer | |||||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / virion membrane / structural molecule activity / RNA binding / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 8.6 Å | |||||||||
Authors | Zhao G / Perilla JR / Yufenyuy E / Meng X / Chen B / Ning J / Ahn J / Gronenborn AM / Schulten K / Aiken C / Zhang P | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5582.map.gz | 932.4 MB | EMDB map data format | |
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Header (meta data) | emd-5582-v30.xml emd-5582.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_5582_1.jpg emd_5582_2.tif | 161.7 KB 583.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5582 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5582 | HTTPS FTP |
-Validation report
Summary document | emd_5582_validation.pdf.gz | 390.7 KB | Display | EMDB validaton report |
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Full document | emd_5582_full_validation.pdf.gz | 390.3 KB | Display | |
Data in XML | emd_5582_validation.xml.gz | 9.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5582 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5582 | HTTPS FTP |
-Related structure data
Related structure data | 3j34MC 3j4fMC 5639C 3j3qC 3j3yC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5582.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Real space helical reconstruction of HIV-1 capsid assembly | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HIV-1 CA A92E
Entire | Name: HIV-1 CA A92E |
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Components |
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-Supramolecule #1000: HIV-1 CA A92E
Supramolecule | Name: HIV-1 CA A92E / type: sample / ID: 1000 / Oligomeric state: helical assembly of hexamers / Number unique components: 6 |
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Molecular weight | Experimental: 25 KDa / Theoretical: 25 KDa |
-Macromolecule #1: HIV-1 capsid protein
Macromolecule | Name: HIV-1 capsid protein / type: protein_or_peptide / ID: 1 / Name.synonym: CA / Oligomeric state: hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Human immunodeficiency virus 1 / synonym: HIV-1 |
Molecular weight | Experimental: 25 KDa / Theoretical: 25 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: Rosetta 2 (DE3) / Recombinant plasmid: pET21 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 / Details: 1 M NaCl, 50 mM Tris-HCl |
Grid | Details: 200 mesh quantifoil R2/1 copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER Method: With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 80 K / Max: 85 K / Average: 82 K |
Date | Dec 11, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 27 / Average electron dose: 15 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 58257 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | The segments were aligned and reconstructed using Frealign. Twofold symmetry was imposed using IHRSR++. |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 7.247 Å Applied symmetry - Helical parameters - Δ&Phi: 31.13 ° Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Frealign |
CTF correction | Details: each filament |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: MDFF |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3j34: PDB-3j4f: |