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- PDB-2ops: Crystal Structure of Y188C Mutant HIV-1 Reverse Transcriptase in ... -

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Basic information

Entry
Database: PDB / ID: 2ops
TitleCrystal Structure of Y188C Mutant HIV-1 Reverse Transcriptase in Complex with GW420867X.
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE / AIDS / NNRTI / GW420867X / DRUG RESISTANCE
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / 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 / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain 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-HBQ / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRen, J. / Nichols, C.E. / Chamberlain, P.P. / Weaver, K.L. / Short, S.A. / Chan, J.H. / Kleim, J. / Stammers, D.K.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Relationship of Potency and Resilience to Drug Resistant Mutations for GW420867X Revealed by Crystal Structures of Inhibitor Complexes for Wild-Type, Leu100Ile, Lys101Glu, and Tyr188Cys Mutant ...Title: Relationship of Potency and Resilience to Drug Resistant Mutations for GW420867X Revealed by Crystal Structures of Inhibitor Complexes for Wild-Type, Leu100Ile, Lys101Glu, and Tyr188Cys Mutant HIV-1 Reverse Transcriptases.
Authors: Ren, J. / Nichols, C.E. / Chamberlain, P.P. / Weaver, K.L. / Short, S.A. / Chan, J.H. / Kleim, J.P. / Stammers, D.K.
History
DepositionJan 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Non-polymer description
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: 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: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9285
Polymers113,4582
Non-polymers4703
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-34 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.500, 110.300, 72.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Reverse transcriptase/ribonuclease H


Mass: 62626.676 Da / Num. of mol.: 1 / Fragment: P66 / Mutation: Y188C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1Subtypes of HIV / Strain: HXB2 ISOLATE / Gene: gag-pol / Plasmid: pkk233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): DG2 / References: UniProt: P04585, RNA-directed DNA polymerase
#2: Protein p51 RT


Mass: 50831.398 Da / Num. of mol.: 1 / Fragment: P51 / Mutation: Y188C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1Subtypes of HIV / Strain: HXB2 ISOLATE / Gene: gag-pol / Plasmid: pkk233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): DG2 / References: UniProt: P04585, RNA-directed DNA polymerase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-HBQ / ISOPROPYL (2S)-2-ETHYL-7-FLUORO-3-OXO-3,4-DIHYDROQUINOXALINE-1(2H)-CARBOXYLATE


Mass: 280.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17FN2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.244 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.244 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 49585 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 53.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4759 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.45 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2232885.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.301 2472 5 %RANDOM
Rwork0.218 ---
obs0.218 49547 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2869 Å2 / ksol: 0.316313 e/Å3
Displacement parametersBiso mean: 59 Å2
Baniso -1Baniso -2Baniso -3
1--6.86 Å20 Å20 Å2
2---10.12 Å20 Å2
3---16.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.32 Å
Luzzati d res low-30 Å
Luzzati sigma a0.51 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7747 0 30 151 7928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.76
X-RAY DIFFRACTIONc_mcangle_it9.6710
X-RAY DIFFRACTIONc_scbond_it10.318
X-RAY DIFFRACTIONc_scangle_it13.9214
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.43 238 5 %
Rwork0.358 4507 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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