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- PDB-1tvr: HIV-1 RT/9-CL TIBO -

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Basic information

Entry
Database: PDB / ID: 1tvr
TitleHIV-1 RT/9-CL TIBO
Components(REVERSE TRANSCRIPTASE) x 2
KeywordsASPARTYL PROTEASE / AIDS / POLYPROTEIN / HYDROLASE / ENDONUCLEASE / RNA-DIRECTED DNA POLYMERASE / 3HIV-1 RT/9-CL TIBO
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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-TB9 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsDas, K. / Ding, J. / Hsiou, Y. / Arnold, E.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant.
Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / ...Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / Michejda, C.J. / Hughes, S.H. / Arnold, E.
#1: Journal: Drug Des.Discovery / Year: 1996
Title: Targeting HIV Reverse Transcriptase for Anti-Aids Drug Design: Structural and Biological Considerations for Chemotherapeutic Strategies
Authors: Arnold, E. / Das, K. / Ding, J. / Yadav, P.N. / Hsiou, Y. / Boyer, P.L. / Hughes, S.H.
#2: Journal: Structure / Year: 1996
Title: Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms
Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Junior, A.D. / Hughes, S.H. / Arnold, E.
#3: Journal: Structure / Year: 1995
Title: Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution
Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / al., et
#4: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors
Authors: Ding, J. / Das, K. / Moereels, H. / Koymans, L. / Andries, K. / Janssen, P.A. / Hughes, S.H. / Arnold, E.
#5: Journal: J.Mol.Biol. / Year: 1994
Title: Locations of Anti-Aids Drug Binding Sites and Resistance Mutations in the Three-Dimensional Structure of HIV-1 Reverse Transcriptase. Implications for Mechanisms of Drug Inhibition and Resistance
Authors: Tantillo, C. / Ding, J. / Jacobo-Molina, A. / Nanni, R.G. / Boyer, P.L. / Hughes, S.H. / Pauwels, R. / Andries, K. / Janssen, P.A. / Arnold, E.
#6: Journal: J.Mol.Recog. / Year: 1994
Title: Buried Surface Analysis of HIV-1 Reverse Transcriptase P66/P51 Heterodimer and its Interaction with DsDNA Template/Primer
Authors: Ding, J. / Jacobo-Molina, A. / Tantillo, C. / Lu, X. / Nanni, R.G. / Arnold, E.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 A Resolution Shows Bent DNA
Authors: Jacobo-Molina, A. / Ding, J. / Nanni, R.G. / Clark Junior, A.D. / Lu, X. / Tantillo, C. / Williams, R.L. / Kamer, G. / Ferris, A.L. / Clark, P. / al., et
History
DepositionApr 16, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REVERSE TRANSCRIPTASE
B: REVERSE TRANSCRIPTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5083
Polymers114,1862
Non-polymers3221
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-37 kcal/mol
Surface area47510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.000, 69.300, 104.100
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein REVERSE TRANSCRIPTASE


Mass: 64274.652 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (CLONE 12)
Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: BH10
Description: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) SUBCLONED FROM BH10 ISOLATE. EXPRESSED AND PROCESSED BY BACTERIAL ESCHERICHIA COLI. REF. A.HIZI, ET AL., (1988) PROC. NATL. ACAD. SCI. USA 85, ...Description: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) SUBCLONED FROM BH10 ISOLATE. EXPRESSED AND PROCESSED BY BACTERIAL ESCHERICHIA COLI. REF. A.HIZI, ET AL., (1988) PROC. NATL. ACAD. SCI. USA 85, 1218-1222. REF. P.K.CLARK, ET AL., (1990) AIDS RES. HUM. RETROVIRUSES 6, 753-764.
Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein REVERSE TRANSCRIPTASE


Mass: 49911.359 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (CLONE 12)
Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: BH10
Description: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) SUBCLONED FROM BH10 ISOLATE. EXPRESSED AND PROCESSED BY BACTERIAL ESCHERICHIA COLI. REF. A.HIZI, ET AL., (1988) PROC. NATL. ACAD. SCI. USA 85, ...Description: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) SUBCLONED FROM BH10 ISOLATE. EXPRESSED AND PROCESSED BY BACTERIAL ESCHERICHIA COLI. REF. A.HIZI, ET AL., (1988) PROC. NATL. ACAD. SCI. USA 85, 1218-1222. REF. P.K.CLARK, ET AL., (1990) AIDS RES. HUM. RETROVIRUSES 6, 753-764.
Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-TB9 / 4-CHLORO-8-METHYL-7-(3-METHYL-BUT-2-ENYL)-6,7,8,9-TETRAHYDRO-2H-2,7,9A-TRIAZA-BENZO[CD]AZULENE-1-THIONE


Mass: 321.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20ClN3S
Compound detailsHIV-1 RT IS COMPOSED OF TWO SUBUNITS OF 66 KDA AND 51 KDA, DESIGNATED AS P66 AND P51, RESPECTIVELY. ...HIV-1 RT IS COMPOSED OF TWO SUBUNITS OF 66 KDA AND 51 KDA, DESIGNATED AS P66 AND P51, RESPECTIVELY. THE POLYMERASE DOMAINS OF BOTH P66 AND P51 CONTAIN OF FOUR SUBDOMAINS, NAMED FINGERS, PALM, THUMB, AND CONNECTION. THE BOUNDARIES OF INDIVIDUAL SUBDOMAINS ARE AS FOLLOWS: FINGERS: 1--84 AND 120--150 PALM: 85--119 AND 151--243 THUMB: 244--322 CONNECTION: 323--437 IN P66 AND 323--427 IN P51.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 65 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop / Details: Clark, A.D., (1995) Methods Enzymol., 262, 171.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
119-20 mg/mlprotein1drop
20.1 %beta-OG1drop
350 mMBis-Tris propane1reservoir
4100 mMammonium sulfate1reservoir
510 %glycerol1reservoir
612 %(w/v)PEG80001reservoir
71.6 %DMSO1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorDetector: CCD / Date: Nov 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionNum. obs: 26209 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 2.16 % / Rmerge(I) obs: 0.064
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 40 Å / Num. measured all: 56695

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 3→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.259 -
obs0.259 21653
Refine analyzeLuzzati coordinate error obs: 0.6 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7824 0 0 21 7845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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