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- PDB-1rti: HIGH RESOLUTION STRUCTURES OF HIV-1 RT FROM FOUR RT-INHIBITOR COM... -

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Entry
Database: PDB / ID: 1rti
TitleHIGH RESOLUTION STRUCTURES OF HIV-1 RT FROM FOUR RT-INHIBITOR COMPLEXES
Components(HIV-1 REVERSE TRANSCRIPTASE) x 2
KeywordsNUCLEOTIDYLTRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / Assembly Of The HIV Virion / RNA-directed DNA polymerase activity / exoribonuclease H activity / Budding and maturation of HIV virion / protein processing / host multivesicular body / 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-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / host cell / viral nucleocapsid / DNA recombination / symbiont-mediated suppression of host gene expression / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / zinc ion binding / identical protein 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. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain 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. / 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
1-(2-HYDROXYETHYLOXYMETHYL)-6-PHENYL THIOTHYMINE / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsRen, J. / Esnouf, R. / Garman, E. / Somers, D. / Ross, C. / Kirby, I. / Keeling, J. / Darby, G. / Jones, Y. / Stuart, D. / Stammers, D.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: High resolution structures of HIV-1 RT from four RT-inhibitor complexes.
Authors: Ren, J. / Esnouf, R. / Garman, E. / Somers, D. / Ross, C. / Kirby, I. / Keeling, J. / Darby, G. / Jones, Y. / Stuart, D.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-Nucleoside Inhibitors
Authors: Esnouf, R. / Ren, J. / Ross, C. / Jones, Y. / Stammers, D. / Stuart, D.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 Angstrom Resolution
Authors: Stammers, D.K. / Somers, D. / Ross, C.K. / Kirby, I. / Ray, P.H. / Wilson, J.E. / Norman, M. / Ren, J.S. / Esnouf, R.M. / Garman, E.F. / Jones, E.Y. / Stuart, D.I.
History
DepositionMay 3, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 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 / diffrn_radiation_wavelength / pdbx_database_status / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE
B: HIV-1 REVERSE TRANSCRIPTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3023
Polymers115,9942
Non-polymers3081
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-31 kcal/mol
Surface area46640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.800, 111.200, 73.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 226 / 2: CIS PROLINE - PRO A 421

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Components

#1: Protein HIV-1 REVERSE TRANSCRIPTASE / HIV-1 RT


Mass: 64594.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXB2 ISOLATE / Cell line: 293 / Gene: HIV-1 POL / Gene (production host): HIV-1 POL / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P04585, RNA-directed DNA polymerase
#2: Protein HIV-1 REVERSE TRANSCRIPTASE / HIV-1 RT


Mass: 51399.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: 293 / Gene: HIV-1 POL / Gene (production host): HIV-1 POL / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P04585, RNA-directed DNA polymerase
#3: Chemical ChemComp-HEF / 1-(2-HYDROXYETHYLOXYMETHYL)-6-PHENYL THIOTHYMINE


Mass: 308.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O4S
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %PEG34001reservoir
2citrate/phosphate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.882 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 5, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.882 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 20390 / % possible obs: 86.3 % / Redundancy: 8.04 % / Rmerge(I) obs: 0.123
Reflection
*PLUS
Num. measured all: 163954 / Rmerge(I) obs: 0.123

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 3→25 Å / σ(F): 0
Details: DUE TO THE LOWER RESOLUTION OF THE DATA, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 20 ANGSTROMS FROM THE CA ATOM OF TYR 188) WERE TIGHTLY RESTRAINED TO THEIR ...Details: DUE TO THE LOWER RESOLUTION OF THE DATA, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 20 ANGSTROMS FROM THE CA ATOM OF TYR 188) WERE TIGHTLY RESTRAINED TO THEIR POSITION IN THE STRUCTURE OF RT AND 1051U91 COMPLEX, AND STRONG STEREOCHEMICAL RESTRAINTS WERE EMPLOYED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rwork0.236 --
obs0.236 20390 86.3 %
Displacement parametersBiso mean: 62 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7836 0 21 0 7857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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