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

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Basic information

Entry
Database: PDB / ID: 3dik
TitlePseudo-atomic model of the HIV-1 CA hexameric lattice
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / MATURE RETROVIRAL CAPSID / FULLERENE CONE / HEXAMER / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Hydrolase / Lipoprotein / Magnesium / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc-finger
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / symbiont-mediated activation of host apoptosis / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / symbiont-mediated activation of host apoptosis / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 9 Å
AuthorsGanser-Pornillos, B.K. / 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 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)24,4981
Polymers24,4981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.700, 92.700, 110.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Capsid protein p24 / Coordinate model: Cα atoms only


Mass: 24498.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1HIV-1 CA PROTEIN R18L MUTANTCOMPLEXSPHERES WERE FLATTENED ON EM GRIDS AND TREATED AS 2D CRYSTALS0
2HIV-1 CA HEXAMERCHAINS A, B, C, D, E, F, G, H, I, J, K, L1
3HIV-1 CA DIMERCHAINS A, B, M, N1
Buffer solutionName: 17.5%(w/v) PEG 20,000, 50mM Na Cacodylate, 100mM Calcium Acetate
pH: 6.5
Details: 17.5%(w/v) PEG 20,000, 50mM Na Cacodylate, 100mM Calcium Acetate
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Carbon coated molybdenum grids
VitrificationCryogen name: ETHANE
Details: Washed with 0.1M KCl, blotted briefly, and plunged into liquid ethane

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 52000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 400 nm / Cs: 2 mm
Specimen holderTemperature: 90 K / Tilt angle max: 40.3 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1SITUS COLACORmodel fitting
2SITUS COLORESmodel fitting
3MRC3D reconstruction
3D reconstructionMethod: 2D crystallography / Resolution: 9 Å
Details: THIS MODDEL CONTAINS CA ATOMS ONLY. THE TWO DOMAINS UNP RESIDUES 133-280 AND UNP RESIDUES 281-351 WERE ALLOWED TO MOVE INDEPENDENTLY. THAT IS WHY THE CONNECTIVITY BETWEEN THEM IS NOT WELL- ...Details: THIS MODDEL CONTAINS CA ATOMS ONLY. THE TWO DOMAINS UNP RESIDUES 133-280 AND UNP RESIDUES 281-351 WERE ALLOWED TO MOVE INDEPENDENTLY. THAT IS WHY THE CONNECTIVITY BETWEEN THEM IS NOT WELL-PRESERVED. MRC AND CCP4 PROGRAMS WERE USED.
Symmetry type: 2D CRYSTAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11GWP

1gwp

11GWP1PDBexperimental model
21A43

1a43

11A432PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms219 0 0 0 219

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