+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1529 | |||||||||
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Title | Structure of Full-Length HIV-1 CA. | |||||||||
Map data | This is a map of full-length HIV-1 CA. | |||||||||
Sample |
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Keywords | HIV-1 / CA / capsid / mature / retrovirus | |||||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | electron crystallography / cryo EM / negative staining / Resolution: 9.0 Å | |||||||||
Authors | Ganser-Pornillos BK / Cheng A / Yeager M | |||||||||
Citation | Journal: Cell / Year: 2007 Title: Structure of full-length HIV-1 CA: a model for the mature capsid lattice. Authors: Barbie K Ganser-Pornillos / Anchi Cheng / Mark Yeager / Abstract: The capsids of mature retroviruses perform the essential function of organizing the viral genome for efficient replication. These capsids are modeled as fullerene structures composed of closed ...The capsids of mature retroviruses perform the essential function of organizing the viral genome for efficient replication. These capsids are modeled as fullerene structures composed of closed hexameric arrays of the viral CA protein, but a high-resolution structure of the lattice has remained elusive. A three-dimensional map of two-dimensional crystals of the R18L mutant of HIV-1 CA was derived by electron cryocrystallography. The docking of high-resolution domain structures into the map yielded the first unambiguous model for full-length HIV-1 CA. Three important protein-protein assembly interfaces are required for capsid formation. Each CA hexamer is composed of an inner ring of six N-terminal domains and an outer ring of C-terminal domains that form dimeric linkers connecting neighboring hexamers. Interactions between the two domains of CA further stabilize the hexamer and provide a structural explanation for the mechanism of action of known HIV-1 assembly inhibitors. | |||||||||
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_1529.map.gz | 5.3 MB | EMDB map data format | |
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Header (meta data) | emd-1529-v30.xml emd-1529.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | 1529.gif | 69.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1529 | HTTPS FTP |
-Validation report
Summary document | emd_1529_validation.pdf.gz | 349.6 KB | Display | EMDB validaton report |
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Full document | emd_1529_full_validation.pdf.gz | 349.1 KB | Display | |
Data in XML | emd_1529_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1529 | HTTPS FTP |
-Related structure data
Related structure data | 3dikMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1529.map.gz / Format: CCP4 / Size: 14.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map of full-length HIV-1 CA. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 1.03 Å / Y: 1.03 Å / Z: 0.92437 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HIV-1 CA R18L
Entire | Name: HIV-1 CA R18L |
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Components |
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-Supramolecule #1000: HIV-1 CA R18L
Supramolecule | Name: HIV-1 CA R18L / type: sample / ID: 1000 / Oligomeric state: 6 / Number unique components: 1 |
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Molecular weight | Experimental: 25 KDa / Theoretical: 25 KDa / Method: mass spectrometry of monomer |
-Macromolecule #1: HIV-1 CA protein
Macromolecule | Name: HIV-1 CA protein / type: protein_or_peptide / ID: 1 / Name.synonym: HIV-1 CA protein / Details: mass spectrometry of virus / 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 plasmid: pET11a |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | electron crystallography |
Aggregation state | 2D array |
-Sample preparation
Concentration | 32 mg/mL |
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Buffer | pH: 6.5 Details: 17.5% (w/v) PEG 20,000, 50mM sodium cacodylate, 100mM Calcium acetate |
Staining | Type: NEGATIVE Details: Grids were absorbed with crystals, washed with 0.1M KCl, blotted, and flash frozen in liquid ethane |
Grid | Details: 300 mesh molybdemun |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Method: blot for 2 sec before plungin |
Details | crstal grown by direct addition of PEG solution |
Crystal formation | Details: crstal grown by direct addition of PEG solution |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 43 / Average electron dose: 15 e/Å2 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 40 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 40 ° |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Software - Name: MRC |
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Crystal parameters | Unit cell - A: 92.7 Å / Unit cell - B: 92.7 Å / Unit cell - C: 110 Å / Unit cell - γ: 120 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Plane group: P 6 |
CTF correction | Details: each image |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Situs |
Details | Protocol: Rigid Body |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT |
Output model | PDB-3dik: |