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- EMDB-1529: Structure of Full-Length HIV-1 CA. -

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Basic information

Entry
Database: EMDB / ID: EMD-1529
TitleStructure of Full-Length HIV-1 CA.
Map dataThis is a map of full-length HIV-1 CA.
Sample
  • Sample: HIV-1 CA R18L
  • Protein or peptide: HIV-1 CA protein
KeywordsHIV-1 / CA / capsid / mature / retrovirus
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
Methodelectron crystallography / cryo EM / negative staining / Resolution: 9.0 Å
AuthorsGanser-Pornillos BK / Cheng A / Yeager M
CitationJournal: 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
DepositionJun 24, 2008-
Header (metadata) releaseJun 24, 2008-
Map releaseApr 2, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 50
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3dik
  • Surface level: 50
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3dik
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1529.gif

Downloads & links

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Map

FileDownload / File: emd_1529.map.gz / Format: CCP4 / Size: 14.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of full-length HIV-1 CA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 121 pix.
= 110. Å		1.03 Å/pix.
x 181 pix.
= 92.7 Å		1.03 Å/pix.
x 181 pix.
= 92.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 1.03 Å / Y: 1.03 Å / Z: 0.92437 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 37.200000000000003 / Movie #1: 50
Minimum - Maximum-241.72999999999999 - 250.0
Average (Standard dev.)-0.138976 (±48.331000000000003)
SymmetrySpace group: 168
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-60
Dimensions181181121
Spacing181181121
CellA: 92.7 Å / B: 92.7 Å / C: 110 Å
α: 90 ° / β: 90 ° / γ: 120 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.030.92436974789916
M x/y/z9090119
origin x/y/z0.0000.0000.000
length x/y/z92.70092.700110.000
α/β/γ90.00090.000120.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S123
start NC/NR/NS-90-90-60
NC/NR/NS181181121
D min/max/mean-241.730250.000-0.139

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Supplemental data

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Sample components

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Entire : HIV-1 CA R18L

EntireName: HIV-1 CA R18L
Components
  • Sample: HIV-1 CA R18L
  • Protein or peptide: HIV-1 CA protein

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Supramolecule #1000: HIV-1 CA R18L

SupramoleculeName: HIV-1 CA R18L / type: sample / ID: 1000 / Oligomeric state: 6 / Number unique components: 1
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa / Method: mass spectrometry of monomer

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Macromolecule #1: HIV-1 CA protein

MacromoleculeName: 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
Source (natural)Organism: Human immunodeficiency virus 1 / synonym: HIV-1
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET11a

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration32 mg/mL
BufferpH: 6.5
Details: 17.5% (w/v) PEG 20,000, 50mM sodium cacodylate, 100mM Calcium acetate
StainingType: NEGATIVE
Details: Grids were absorbed with crystals, washed with 0.1M KCl, blotted, and flash frozen in liquid ethane
GridDetails: 300 mesh molybdemun
VitrificationCryogen name: ETHANE / Instrument: OTHER / Method: blot for 2 sec before plungin
Detailscrstal grown by direct addition of PEG solution
Crystal formationDetails: crstal grown by direct addition of PEG solution

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000
Sample stageSpecimen 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 °
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Image recordingCategory: 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 min0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Crystal parametersUnit 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 correctionDetails: each image
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Software - Name: MRC

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Atomic model buiding 1

Initial modelPDB ID:

1gwp

SoftwareName: Situs
DetailsProtocol: Rigid Body
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-3dik:
Pseudo-atomic model of the HIV-1 CA hexameric lattice

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Atomic model buiding 2

Initial modelPDB ID:

1a43

SoftwareName: Situs
DetailsProtocol: Rigid Body
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-3dik:
Pseudo-atomic model of the HIV-1 CA hexameric lattice

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