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

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Entry
Database: PDB / ID: 1dlo
TitleHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
Components(HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE) x 2
KeywordsNUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / 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 ...RNA-directed DNA polymerase activity / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsHsiou, Y. / Ding, J. / Das, K. / Hughes, S. / Arnold, E.
Citation
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 Jr., A.D. / Hughes, S.H. / Arnold, E.
#1: 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
#2: 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.J. / Hughes, S.H. / Arnold, E.
#3: 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 17, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: 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 / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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
Revision 1.4Feb 7, 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: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE
B: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE


Theoretical massNumber of molelcules
Total (without water)113,9002
Polymers113,9002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-20 kcal/mol
Surface area43890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.500, 70.300, 93.300
Angle α, β, γ (deg.)90.00, 106.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE / HIV-1 RT


Mass: 63988.273 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH10 ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE / HIV-1 RT


Mass: 49911.359 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH10 ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
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 FOLLOWING: 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. THE CURRENT MODEL CONTAINS 556 AMINO ACID RESIDUES (1 - 556) AND 4370 NON-HYDROGEN ATOMS FOR P66, 427 AMINO ACID RESIDUES (1 - 427) AND 3322 NON-HYDROGEN ATOMS FOR P51. 267 WATER MOLECULES WERE INCLUDED IN THE CURRENT REFINEMENT. THE BETA 3 - BETA 4 LOOP (65 - 72), BETA 7 - BETA 8 LOOP (133 - 143), THE REGION FROM BETA 14 TO ALPHA H (249 - 258), AND ALPHA I - ALPHA J LOOP (281 - 293) OF P66, ARE HIGHLY DISORDERED WITH VERY POOR ELECTRON DENSITY, THEREFORE, THE BACKBONE TRACES IN THESE REGIONS ARE TENTATIVE. THE LOOP BETWEEN ALPHA F AND BETA 13 (219 - - 230) OF P51 HAS NO ELECTRON DENSITY AND THUS HAS NOT BEEN MODELED. DUE TO THE VERY WEAK OR INVISIBLE ELECTRON DENSITY FOR THE SIDE CHAINS, THE FOLLOWING RESIDUES HAVE BEEN MODELED AS ALANINES DURING THE REFINEMENT BUT ARE GIVEN THEIR CORRECT RESIDUE NAMES IN THIS ENTRY. P66 (CHAIN A): 22, 28, 64, 70 - 71, 134 - 136, 139, 169, 177, 194, 203, 218, 224, 242, 278, 281, 291, 297, 305, 311 - 312, 334, 336, 356 - 359, 404, 407, 413 - 414, 424, 448, 451, 512, 514, 527, 549 - 551, 556. P51 (CHAIN B): 36, 67 - 69, 88 - 89, 173, 197, 238, 281 - 282, 295, 297, 305 - 306, 308, 356 - 358, 361 - 362, 407, 424 - 425, 427. THE DEFINITION OF SECONDARY STRUCTURAL ELEMENTS IS LARGELY BASED ON PROGRAM PROCHECK AND HYDROGEN-BONDING PATTERN. THE NAMES OF SECONDARY STRUCTURAL ELEMENTS WERE BASICALLY KEPT CONSISTENT WITH THAT THE DEPOSITORS USED IN JACOBO-MOLINA ET AL. (1993). SOME ASSIGNED BETA STRANDS DO NOT APPEAR TO PARTICIPATE IN BETA SHEETS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 64 %
Crystal
*PLUS
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

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.908
DetectorDetector: IMAGE PLATE AREA DETECTOR / Date: Oct 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionNum. obs: 41049 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 142770

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.7→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.336 -
Rwork0.249 -
obs0.249 38310
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7692 0 0 267 7959
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
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 / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.01

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