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- PDB-3hvt: STRUCTURAL BASIS OF ASYMMETRY IN THE HUMAN IMMUNODEFICIENCY VIRUS... -

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Basic information

Entry
Database: PDB / ID: 3hvt
TitleSTRUCTURAL BASIS OF ASYMMETRY IN THE HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE HETERODIMER
Components
  • HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
  • HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
KeywordsNUCLEOTIDYLTRANSFERASE
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 / host multivesicular body / 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 / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / 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-NVP / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsSteitz, T.A. / Smerdon, S.J. / Jaeger, J. / Wang, J. / Kohlstaedt, L.A. / Chirino, A.J. / Friedman, J.M. / Rice, P.A.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 1994
Title: Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1.
Authors: Smerdon, S.J. / Jager, J. / Wang, J. / Kohlstaedt, L.A. / Chirino, A.J. / Friedman, J.M. / Rice, P.A. / Steitz, T.A.
#1: Journal: To be Published
Title: Comparison of Three Different Crystal Forms Shows HIV-1 Reverse Transcriptase Displays an Internal Swivel Motion
Authors: Jaeger, J. / Smerdon, S.J. / Wang, J. / Boisvert, D.C. / Steitz, T.A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of the Binding Site for Nonnucleoside Inhibitors of the Reverse Transcriptase of Human Immunodeficiency Virus Type 1
Authors: Smerdon, S.J. / Jaeger, J. / Wang, J. / Kohlstaedt, L.A. / Chirino, A.J. / Friedman, J. / Rice, P.A. / Steitz, T.A.
#3: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1993
Title: Two DNA Polymerases: HIV Reverse Transcriptase and Klenow Fragment of E. Coli DNA Polymerase I. (In: DNA & Chromosomes: Abstracts of Papers Presented at the LVIII Cold Spring Harbor Symposium ...Title: Two DNA Polymerases: HIV Reverse Transcriptase and Klenow Fragment of E. Coli DNA Polymerase I. (In: DNA & Chromosomes: Abstracts of Papers Presented at the LVIII Cold Spring Harbor Symposium on Quantitative Biology)
Authors: Steitz, T.A. / Smerdon, S.J. / Jaeger, J. / Wang, J. / Kohlstaedt, L.A. / Friedman, J. / Beese, L. / Rice, P.A.
#4: Journal: Science / Year: 1992
Title: Crystal Structure at 3.5 Angstroms Resolution of HIV-1 Reverse Transcriptase Complexed with an Inhibitor
Authors: Kohlstaedt, L.A. / Wang, J. / Friedman, J.M. / Rice, P.A. / Steitz, T.A.
History
DepositionJul 25, 1994Processing site: BNL
SupersessionOct 15, 1994ID: 2HVT
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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 REVERSE TRANSCRIPTASE (SUBUNIT P66)
B: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3263
Polymers114,0602
Non-polymers2661
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-27 kcal/mol
Surface area46920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.600, 69.900, 105.500
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO B 4 / 2: CIS PROLINE - PRO B 294 / 3: CIS PROLINE - PRO B 420

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Components

#1: Protein HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)


Mass: 64004.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)


Mass: 50055.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-NVP / 11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE / NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE


Mass: 266.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N4O / Comment: medication*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion / Details: Kohlstaedt, L.A., (1992) Science, 256, 1783.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16-8 mg/mlRT1drop
225 mMBis-Tris propane1drop
350 mM1drop(NH4)2SO4
40.1 %(w/v)beta-octylglucoside1drop
55 %(v/v)glycerol1drop
67 %(w/v)PEG80001drop
70.01 %sodium azide1drop
850 mMBis-Tris propane1reservoir
9100 mM1reservoir(NH4)2SO4
100.2 %(w/v)beta-octylglucoside1reservoir
1110 %(v/v)glycerol1reservoir
1214 %(w/v)PEG80001reservoir
130.02 %sodium azide1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 33169 / % possible obs: 0.96 % / Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.266 -
obs0.266 31265
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7406 0 20 0 7426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.5
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
Rfactor obs: 0.266 / Rfactor Rwork: 0.266
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.5

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