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- PDB-4puo: Crystal structure of HIV-1 reverse transcriptase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4puo
TitleCrystal structure of HIV-1 reverse transcriptase in complex with RNA/DNA and Nevirapine
Components
  • 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3'
  • 5'-R(P*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'
  • HIV-1 Reverse Transcriptase, p51 subunit
  • HIV-1 Reverse Transcriptase, p66 subunit
KeywordsTRANSFERASE / HYDROLASE/DNA/RNA/INHIBITOR / fingers / palm / thumb / connection / RNase H / nucleotidyltransferase / DNA-directed DNA polymerase / RNA-directed DNA polymerase / Nuclease / Ribonuclease H / tRNA / HYDROLASE-DNA-RNA-INHIBITOR complex
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-NVP / DNA / DNA (> 10) / RNA / RNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsDas, K. / Martinez, S.E. / Arnold, E.
Citation
Journal: Nucleic Acids Res. / Year: 2014
Title: Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.
Authors: Das, K. / Martinez, S.E. / Bandwar, R.P. / Arnold, E.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
Authors: Das, K. / Martinez, S.E. / Bauman, J.D. / Arnold, E.
#2: Journal: J.Biol.Chem. / Year: 2009
Title: Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance.
Authors: Das, K. / Bandwar, R.P. / White, K.L. / Feng, J.Y. / Sarafianos, S.G. / Tuske, S. / Tu, X. / Clark, A.D. / Boyer, P.L. / Hou, X. / Gaffney, B.L. / Jones, R.A. / Miller, M.D. / Hughes, S.H. / Arnold, E.
#3: Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis of HIV-1 resistance to AZT by excision.
Authors: Tu, X. / Das, K. / Han, Q. / Bauman, J.D. / Clark, A.D. / Hou, X. / Frenkel, Y.V. / Gaffney, B.L. / Jones, R.A. / Boyer, P.L. / Hughes, S.H. / Sarafianos, S.G. / Arnold, E.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.
Authors: Das, K. / Bauman, J.D. / Clark, A.D. / Frenkel, Y.V. / Lewi, P.J. / Shatkin, A.J. / Hughes, S.H. / Arnold, E.
#5: Journal: Embo J. / Year: 2001
Title: Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
Authors: Sarafianos, S.G. / Das, K. / Tantillo, C. / Clark, A.D. / Ding, J. / Whitcomb, J.M. / Boyer, P.L. / Hughes, S.H. / Arnold, E.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 Reverse Transcriptase, p66 subunit
B: HIV-1 Reverse Transcriptase, p51 subunit
C: HIV-1 Reverse Transcriptase, p66 subunit
D: HIV-1 Reverse Transcriptase, p51 subunit
T: 5'-R(P*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'
E: 5'-R(P*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'
P: 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3'
F: 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,00710
Polymers258,4758
Non-polymers5332
Water00
1
A: HIV-1 Reverse Transcriptase, p66 subunit
B: HIV-1 Reverse Transcriptase, p51 subunit
T: 5'-R(P*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'
P: 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,5045
Polymers129,2374
Non-polymers2661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-56 kcal/mol
Surface area51880 Å2
MethodPISA
2
C: HIV-1 Reverse Transcriptase, p66 subunit
D: HIV-1 Reverse Transcriptase, p51 subunit
E: 5'-R(P*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'
F: 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,5045
Polymers129,2374
Non-polymers2661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-58 kcal/mol
Surface area52430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.736, 132.128, 141.961
Angle α, β, γ (deg.)90.00, 100.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIV-1 Reverse Transcriptase, p66 subunit / Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT


Mass: 64022.414 Da / Num. of mol.: 2 / Fragment: UNP residues 600-1153 / Mutation: Q258C, C280S, D498N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein HIV-1 Reverse Transcriptase, p51 subunit / p51 RT


Mass: 50039.488 Da / Num. of mol.: 2 / Fragment: UNP residues 600-1027 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase
#3: RNA chain 5'-R(P*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'


Mass: 8759.271 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: DNA chain 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3'


Mass: 6416.122 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: 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.: 2 / Source method: obtained synthetically / Formula: C15H14N4O / Comment: medication*YM

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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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 9-11% PEG8000, 100 mM ammonium sulfate, 5% glycerol, 5% sucrose, 20 mM magnesium chloride, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.915 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 71012 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.8
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 1.27 / Num. unique all: 3336 / % possible all: 94.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V81

3v81


Resolution: 2.901→46.508 Å / SU ML: 0.51 / σ(F): 0 / Phase error: 30.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2854 2135 3.01 %
Rwork0.2281 --
obs0.2298 70967 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.901→46.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15818 1604 40 0 17462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01518092
X-RAY DIFFRACTIONf_angle_d1.77224934
X-RAY DIFFRACTIONf_dihedral_angle_d19.7187003
X-RAY DIFFRACTIONf_chiral_restr0.0752747
X-RAY DIFFRACTIONf_plane_restr0.0122866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-2.96850.39111450.3544109X-RAY DIFFRACTION90
2.9685-3.04270.35881340.34324482X-RAY DIFFRACTION97
3.0427-3.1250.351340.33674607X-RAY DIFFRACTION99
3.125-3.21690.38181540.30984618X-RAY DIFFRACTION99
3.2169-3.32070.36231500.30014635X-RAY DIFFRACTION100
3.3207-3.43930.31771260.28824632X-RAY DIFFRACTION100
3.4393-3.5770.31681370.24864626X-RAY DIFFRACTION100
3.577-3.73970.2891680.22834655X-RAY DIFFRACTION100
3.7397-3.93680.26421240.20434637X-RAY DIFFRACTION100
3.9368-4.18330.26161600.18484618X-RAY DIFFRACTION100
4.1833-4.50610.23771480.17544672X-RAY DIFFRACTION100
4.5061-4.95910.2431490.18284657X-RAY DIFFRACTION100
4.9591-5.67560.24541480.2034673X-RAY DIFFRACTION100
5.6756-7.14640.31781290.23054700X-RAY DIFFRACTION100
7.1464-46.51380.24641290.19654511X-RAY DIFFRACTION94

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