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- PDB-3dtj: HIV-1 capsid C-terminal domain mutant (E187A) -

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Basic information

Entry
Database: PDB / ID: 3dtj
TitleHIV-1 capsid C-terminal domain mutant (E187A)
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV / CAPSID / MUTANT / INHIBITOR / ASSEMBLY / POLYPROTEIN / COMPLEX(VIRAL PROTEIN-PEPTIDE) / MAINLY ALPHA
Function / homology
Function and homology information


viral budding via host ESCRT complex / HIV-1 retropepsin / 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 budding via host ESCRT complex / HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Retrovirus capsid C-terminal domain / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain ...Retrovirus capsid C-terminal domain / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsIgonet, S. / Vaney, M.C. / Rey, F.A.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Residues in the HIV-1 Capsid Assembly Inhibitor Binding Site Are Essential for Maintaining the Assembly-competent Quaternary Structure of the Capsid Protein.
Authors: Bartonova, V. / Igonet, S. / Sticht, J. / Glass, B. / Habermann, A. / Vaney, M.C. / Sehr, P. / Lewis, J. / Rey, F.A. / Krausslich, H.G.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The HIV-1 capsid protein C-terminal domain in complex with a virus assembly inhibitor
Authors: Ternois, F. / Sticht, J. / Duquerroy, S. / Krausslich, H.-G. / Rey, F.A.
History
DepositionJul 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Refinement description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 capsid protein
B: HIV-1 capsid protein
C: HIV-1 capsid protein
D: HIV-1 capsid protein


Theoretical massNumber of molelcules
Total (without water)37,8924
Polymers37,8924
Non-polymers00
Water00
1
C: HIV-1 capsid protein
D: HIV-1 capsid protein


Theoretical massNumber of molelcules
Total (without water)18,9462
Polymers18,9462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-12 kcal/mol
Surface area7940 Å2
MethodPISA
2
A: HIV-1 capsid protein
B: HIV-1 capsid protein


Theoretical massNumber of molelcules
Total (without water)18,9462
Polymers18,9462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.603, 51.675, 51.797
Angle α, β, γ (deg.)109.94, 108.48, 110.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
HIV-1 capsid protein


Mass: 9472.884 Da / Num. of mol.: 4 / Fragment: C-terminal domain, UNP residues 278-363 / Mutation: E187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: gag / Plasmid: pET11c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPLus-RIL / References: UniProt: Q72497, UniProt: P12497*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5
Details: 32% PEG 4,000, 100 mM ammonium acetate pH 5.0 and 10 mM MgCl2., EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.044 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2005 / Details: Dynamically bendable mirror
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 4→30.2 Å / Num. obs: 2160 / % possible obs: 62.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 12.4

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Processing

Software
NameClassification
RemDAqdata collection
PHASERphasing
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DS5

3ds5


Resolution: 4→30.2 Å / σ(F): 0 / σ(I): 0
Details: No refinement was undertaken because of the low resolution data. Only molecular replacement with the 3D model 3DS5 (HIV-1 C-terminal domain capsid mutant (N183A)) gave a solution with the ...Details: No refinement was undertaken because of the low resolution data. Only molecular replacement with the 3D model 3DS5 (HIV-1 C-terminal domain capsid mutant (N183A)) gave a solution with the same packing of the molecules.
Refinement stepCycle: LAST / Resolution: 4→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 0 0 2288

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