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

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Basic information

Entry
Database: PDB / ID: 4pwd
TitleCrystal structure of HIV-1 reverse transcriptase in complex with bulge-RNA/DNA and Nevirapine
Components
  • (HIV-1 Reverse Transcriptase, ...) x 2
  • 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(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*U)-3'
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


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 / RNA-directed DNA polymerase / viral genome integration into host DNA ...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 / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / telomerase activity / 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 / viral translational frameshifting / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / 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. / 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
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: 3 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 19, 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 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*U)-3'
E: 5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*U)-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)259,15113
Polymers258,4438
Non-polymers7095
Water00
1
A: HIV-1 Reverse Transcriptase, P66 subunit
B: HIV-1 Reverse Transcriptase, P51 subunit
T: 5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*U)-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)129,6247
Polymers129,2214
Non-polymers4023
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-91 kcal/mol
Surface area51760 Å2
MethodPISA
2
C: HIV-1 Reverse Transcriptase, P66 subunit
D: HIV-1 Reverse Transcriptase, P51 subunit
E: 5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*U)-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)129,5286
Polymers129,2214
Non-polymers3062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-86 kcal/mol
Surface area51690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.684, 130.765, 141.866
Angle α, β, γ (deg.)90.00, 100.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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HIV-1 Reverse Transcriptase, ... , 2 types, 4 molecules ACBD

#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

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RNA chain / DNA chain , 2 types, 4 molecules TEPF

#3: RNA chain 5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*U)-3'


Mass: 8743.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA template
#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 / Details: DNA primer

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Non-polymers , 3 types, 5 molecules

#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, antiretroviral*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 %
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 7.2-7.4, 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: Nov 18, 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: 3→50 Å / Num. all: 64540 / Num. obs: 61963 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3219 / % possible all: 90.9

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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: 3→44.678 Å / SU ML: 0.54 / σ(F): 0 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2909 1837 2.96 %
Rwork0.2213 --
all0.2234 --
obs0.2234 61963 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→44.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15812 1649 47 0 17508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01518140
X-RAY DIFFRACTIONf_angle_d1.64925011
X-RAY DIFFRACTIONf_dihedral_angle_d19.4977022
X-RAY DIFFRACTIONf_chiral_restr0.0762757
X-RAY DIFFRACTIONf_plane_restr0.0112867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.08110.40151220.35364354X-RAY DIFFRACTION91
3.0811-3.17170.44431440.33244337X-RAY DIFFRACTION91
3.1717-3.27410.3071350.31064406X-RAY DIFFRACTION92
3.2741-3.39110.32771330.28554500X-RAY DIFFRACTION94
3.3911-3.52680.34251490.26154522X-RAY DIFFRACTION95
3.5268-3.68720.30581420.24454625X-RAY DIFFRACTION96
3.6872-3.88150.29711320.21984695X-RAY DIFFRACTION98
3.8815-4.12450.2851430.20094752X-RAY DIFFRACTION99
4.1245-4.44270.23881540.18524773X-RAY DIFFRACTION99
4.4427-4.88930.26781420.17964813X-RAY DIFFRACTION100
4.8893-5.59570.27631320.19394840X-RAY DIFFRACTION100
5.5957-7.04550.29711570.22064809X-RAY DIFFRACTION100
7.0455-44.6830.24471520.17994700X-RAY DIFFRACTION95

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