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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 / homologyZinc finger, CCHC-type / Peptidase A2A, retrovirus, catalytic / Zinc finger, CCHC-type superfamily / Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H superfamily / Immunodeficiency lentiviral matrix, N-terminal / Reverse transcriptase domain / Retroviral nucleocapsid protein Gag / Integrase, C-terminal, retroviral / Integrase, catalytic core ...Zinc finger, CCHC-type / Peptidase A2A, retrovirus, catalytic / Zinc finger, CCHC-type superfamily / Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H superfamily / Immunodeficiency lentiviral matrix, N-terminal / Reverse transcriptase domain / Retroviral nucleocapsid protein Gag / Integrase, C-terminal, retroviral / Integrase, catalytic core / Aspartic peptidase, active site / Ribonuclease H domain / Retroviral aspartyl protease / Integrase, N-terminal zinc-binding domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Reverse transcriptase connection / Reverse transcriptase thumb / Retroviral matrix protein / Ribonuclease H-like superfamily / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Integrase-like, N-terminal / Retropepsins / Retropepsin-like catalytic domain / RNase H / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase connection domain / Integrase DNA binding domain profile. / Integrase catalytic domain profile. / RNase H domain profile. / Reverse transcriptase (RT) catalytic domain profile. / Zinc finger integrase-type profile. / Aspartyl protease, retroviral-type family profile. / Zinc finger CCHC-type profile. / Eukaryotic and viral aspartyl proteases active site. / Reverse transcriptase thumb domain / Zinc knuckle / Aspartic peptidase domain superfamily / Integrase Zinc binding domain / Integrase core domain / gag gene protein p24 (core nucleocapsid protein) / Integrase DNA binding domain / gag gene protein p17 (matrix protein) / phosphatidylinositol-4,5-bisphosphate binding / induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H activity / exoribonuclease H / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase / DNA integration / viral genome integration into host DNA / Nucleotidyltransferases / RNA-directed DNA polymerase activity / suppression by virus of host gene expression / RNA-DNA hybrid ribonuclease activity / establishment of integrated proviral latency / viral entry into host cell / viral nucleocapsid / lipid binding / DNA recombination / Acting on Ester Bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / magnesium ion binding / protein homodimerization activity / RNA binding / DNA binding / zinc ion binding / identical protein binding / Gag-Pol polyprotein
Function and homology information
Specimen sourceHuman immunodeficiency virus type 1
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / 9 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2008 / Release: Sep 16, 2008
RevisionDateData content typeGroupProviderType
1.0Sep 16, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)24,4981
Polyers24,4981
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
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-MP 6

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Components

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


Mass: 24498.084 Da / Num. of mol.: 1 / Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Plasmid name: 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 / 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
Details: 17.5%(w/v) PEG 20,000, 50mM Na Cacodylate, 100mM Calcium Acetate
pH: 6.5
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
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 52000 / Nominal defocus max: 1500 nm / Nominal defocus min: 400 nm / Cs: 2 mm
Specimen holderTemperature: 90 kelvins / Tilt angle max: 40.3 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m 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-PRESERVED. MRC AND CCP4 PROGRAMS WERE USED.
Symmetry type: 2D CRYSTAL
Atomic model buildingDetails: REFINEMENT PROTOCOL--RIGID BODY / Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11GWP1
21A431
Number of atoms included #LASTProtein: 219 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 219

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