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- PDB-2buo: HIV-1 capsid C-terminal domain in complex with an inhibitor of pa... -

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Basic information

Entry
Database: PDB / ID: 2buo
TitleHIV-1 capsid C-terminal domain in complex with an inhibitor of particle assembly
Components
  • HIV-1 CAPSID PROTEIN
  • INHIBITOR OF CAPSID ASSEMBLY
KeywordsVIRAL PROTEIN/PEPTIDE / HIV / CAPSID / INHIBITOR / ASSEMBLY / POLYPROTEIN / COMPLEX (VIRAL PROTEIN-PEPTIDE) / VIRAL PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / identical protein 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 / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal 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 / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTernois, F. / Sticht, J. / Duquerroy, S. / Krausslich, H.-G. / Rey, F.A.
Citation
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.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: A Peptide Inhibitor of HIV-1 Assembly in Vitro
Authors: Sticht, J. / Humbert, M. / Findlow, S. / Bodem, J. / Muller, D. / Dietrich, U. / Werner, J. / Krausslich, H.-G.
History
DepositionJun 17, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 CAPSID PROTEIN
T: INHIBITOR OF CAPSID ASSEMBLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0373
Polymers10,9762
Non-polymers601
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.541, 42.541, 90.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HIV-1 CAPSID PROTEIN


Mass: 9530.921 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 278-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: NL4-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72497, UniProt: P03347*PLUS
#2: Protein/peptide INHIBITOR OF CAPSID ASSEMBLY


Mass: 1445.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growDetails: 32% PEG 4000 100MM AMMONIUM SULFATE PH4.6 10MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 9669 / % possible obs: 99.4 % / Observed criterion σ(I): -2 / Redundancy: 9 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A43

1a43


Resolution: 1.7→20 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1019592.08 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 480 4.9 %RANDOM
Rwork0.224 ---
obs0.224 9669 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.5939 Å2 / ksol: 0.317995 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.83 Å20 Å20 Å2
2--5.83 Å20 Å2
3----11.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 0 4 124 878
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 79 5.1 %
Rwork0.304 1475 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ACY_XPLOR_PAR.TXTACY_XPLOR_TOP.TXT

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