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- PDB-1hpz: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 -

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Basic information

Entry
Database: PDB / ID: 1hpz
TitleHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
Components(POL POLYPROTEIN) x 2
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / 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-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / 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 / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Nucleotidyltransferase; domain 5 / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AAP / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDing, J. / Hsiou, Y. / Arnold, E.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance.
Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Jr., A.D. / Boyer, P.L. / Lewi, P. / Janssen, P.A. / Kleim, J.P. / Rosner, M. / Hughes, S.H. / Arnold, E.
#1: Journal: Structure / Year: 1995
Title: Structure of HIV-1 Reverse Transcriptase in a Complex with the Nonnucleoside Inhibitor Alpha-APA R95845 at 2.8 A Resolution
Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Jr., A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K.
History
DepositionDec 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 9, 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

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Assembly

Deposited unit
A: POL POLYPROTEIN
B: POL POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1043
Polymers114,7532
Non-polymers3511
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-33 kcal/mol
Surface area47260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.1, 69.0, 104.0
Angle α, β, γ (deg.)90, 106.8, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein POL POLYPROTEIN / REVERSE TRANSCRIPTASE


Mass: 64485.887 Da / Num. of mol.: 1 / Fragment: P66 SUBUNIT / Mutation: K103N, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: HIV-1 CLONE 12; / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 ISOLATE / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein POL POLYPROTEIN / REVERSE TRANSCRIPTASE


Mass: 50266.684 Da / Num. of mol.: 1 / Fragment: P51 SUBUNIT / Mutation: K103N, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: HIV-1 CLONE 12 / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 ISOLATE / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-AAP / ALPHA-(2,6-DICHLOROPHENYL)-ALPHA-(2-ACETYL-5-METHYLANILINO)ACETAMIDE


Mass: 351.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16Cl2N2O2

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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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Bis-Tris.propane, ammoniun sulfate, glycerol, PEG 8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMNNRTI1drop
25 %(w/v)beta-OG1drop
330 mg/mlprotein1drop
410 mMTris-HCl1drop
575 mM1dropNaCl
650 mMbis-Tris-propane1reservoir
7100 mMammonium sulfate1reservoir
810 %(w/v)glycerol1reservoir
9DMSO1drop
109 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 195243 / Num. obs: 29927 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 7
Reflection shellResolution: 3→3.05 Å / Redundancy: 5 % / Rmerge(I) obs: 0.38 / % possible all: 93.7
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 195243
Reflection shell
*PLUS
% possible obs: 94.2 % / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HNI

1hni


Resolution: 3→25 Å / σ(F): 2 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.343 1397 4.56 %random
Rwork0.254 ---
obs-28432 92.8 %-
Displacement parametersBiso mean: 65.4 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7798 0 23 0 7821
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_improper_angle_d1.4
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 25 Å / σ(F): 2 / % reflection Rfree: 4.56 % / Rfactor obs: 0.259
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 65.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / Rfactor Rfree: 0.356 / Rfactor obs: 0.345

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