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- PDB-2pwo: Crystal Structure of HIV-1 CA146 A92E Psuedo Cell -

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Basic information

Entry
Database: PDB / ID: 2pwo
TitleCrystal Structure of HIV-1 CA146 A92E Psuedo Cell
ComponentsGag-Pol polyprotein (Pr160Gag-Pol)
KeywordsVIRAL PROTEIN / Viral Capsid / HIV-1 / Anti-Viral
Function / homology
Function and homology information


viral process / HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...viral process / 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 / viral capsid / 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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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 ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKelly, B.N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of the Antiviral Assembly Inhibitor CAP-1 Complex with the HIV-1 CA Protein.
Authors: Kelly, B.N. / Kyere, S. / Kinde, I. / Tang, C. / Howard, B.R. / Robinson, H. / Sundquist, W.I. / Summers, M.F. / Hill, C.P.
History
DepositionMay 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gag-Pol polyprotein (Pr160Gag-Pol)
B: Gag-Pol polyprotein (Pr160Gag-Pol)
C: Gag-Pol polyprotein (Pr160Gag-Pol)
D: Gag-Pol polyprotein (Pr160Gag-Pol)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1928
Polymers65,0504
Non-polymers1424
Water9,602533
1
A: Gag-Pol polyprotein (Pr160Gag-Pol)
B: Gag-Pol polyprotein (Pr160Gag-Pol)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5964
Polymers32,5252
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Gag-Pol polyprotein (Pr160Gag-Pol)
D: Gag-Pol polyprotein (Pr160Gag-Pol)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5964
Polymers32,5252
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.225, 48.208, 58.928
Angle α, β, γ (deg.)83.01, 71.28, 87.43
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a hexamer

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Components

#1: Protein
Gag-Pol polyprotein (Pr160Gag-Pol)


Mass: 16262.610 Da / Num. of mol.: 4 / Fragment: N-Terminal Domain / Mutation: A92E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: NL4-3 / Gene: gag-pol / Plasmid: CA146 A92E Pet11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12497, UniProt: A9PKC6*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24% PEG 4500, 0.60 M MgCl2, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 84854 / Num. obs: 77217 / % possible obs: 91 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.056 / Χ2: 1.718 / Net I/σ(I): 14
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2 / Num. unique all: 5216 / Χ2: 0.702 / % possible all: 61.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CA146

Resolution: 1.45→30.03 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.91 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.12 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3881 5 %RANDOM
Rwork0.17 ---
obs0.173 77215 90.72 %-
all-84854 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.03 Å2-0.04 Å2
2--0.3 Å20.08 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4828 0 4 533 5365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214984
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9336842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.24825.193233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6515893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2351530
X-RAY DIFFRACTIONr_chiral_restr0.110.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023882
X-RAY DIFFRACTIONr_nbd_refined0.2380.22565
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.2375
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.2172
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.241
X-RAY DIFFRACTIONr_mcbond_it1.8011.53156
X-RAY DIFFRACTIONr_mcangle_it2.57525056
X-RAY DIFFRACTIONr_scbond_it3.53732065
X-RAY DIFFRACTIONr_scangle_it5.1334.51756
X-RAY DIFFRACTIONr_rigid_bond_restr2.08335221
X-RAY DIFFRACTIONr_sphericity_free8.1533538
X-RAY DIFFRACTIONr_sphericity_bonded5.3634828
LS refinement shellResolution: 1.45→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 159 -
Rwork0.19 3347 -
obs-3506 55.38 %

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