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- PDB-4q0b: Crystal structure of HIV-1 reverse transcriptase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4q0b
TitleCrystal structure of HIV-1 reverse transcriptase in complex with gap-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*G)-3'
  • 5'-R(P*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'
KeywordsTRANSFERASE / HYDROLASE/RNA/DNA/INHIBITOR / fingers / palm / thumb / connection / RNase H / nucleotidyltransferase / DNA-directed DNA polymerase / RNA-directed DNA polymerase / ribonuclease H / tRNA / HYDROLASE-RNA-DNA-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: 3.3 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
DepositionApr 1, 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_conn / struct_ref / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref.pdbx_seq_one_letter_code / _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*G)-3'
t: 5'-R(P*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'
E: 5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*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'
e: 5'-R(P*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,46515
Polymers257,72610
Non-polymers7395
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*G)-3'
t: 5'-R(P*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)129,1847
Polymers128,8635
Non-polymers3212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-61 kcal/mol
Surface area51140 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*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'
e: 5'-R(P*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,2808
Polymers128,8635
Non-polymers4173
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-76 kcal/mol
Surface area51630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.716, 131.051, 141.631
Angle α, β, γ (deg.)90.00, 100.69, 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


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


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 , 2 types, 4 molecules TEte

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


Mass: 4493.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: gap-RNA template
#4: RNA chain 5'-R(P*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3'


Mass: 3891.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: gap-RNA template

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DNA chain , 1 types, 2 molecules PF

#5: 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

#6: 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
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#8: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.14 %
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: Oct 13, 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: 3.3→50 Å / Num. all: 49011 / Num. obs: 48325 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 7
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.38 / Num. unique all: 2355 / % possible all: 97.6

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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: 3.3→46.391 Å / SU ML: 0.62 / σ(F): 0 / Phase error: 34.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3172 1419 2.97 %RANDOM
Rwork0.2348 ---
all0.2373 48541 --
obs0.2373 47852 98.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→46.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15818 1563 47 0 17428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01318037
X-RAY DIFFRACTIONf_angle_d1.7724841
X-RAY DIFFRACTIONf_dihedral_angle_d20.1836973
X-RAY DIFFRACTIONf_chiral_restr0.0722735
X-RAY DIFFRACTIONf_plane_restr0.0122864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2999-3.41790.38871290.35324558X-RAY DIFFRACTION98
3.4179-3.55470.39371610.33084585X-RAY DIFFRACTION98
3.5547-3.71640.41191340.29824597X-RAY DIFFRACTION98
3.7164-3.91220.34011340.25354630X-RAY DIFFRACTION99
3.9122-4.15720.31041420.22524628X-RAY DIFFRACTION99
4.1572-4.47790.25411520.19714668X-RAY DIFFRACTION99
4.4779-4.92810.30031340.19034687X-RAY DIFFRACTION99
4.9281-5.64010.30721310.2034706X-RAY DIFFRACTION99
5.6401-7.10190.30591550.24954697X-RAY DIFFRACTION100
7.1019-46.39530.28751470.19994677X-RAY DIFFRACTION97

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