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- PDB-3dok: Crystal structure of K103N mutant HIV-1 reverse transcriptase in ... -

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Basic information

Entry
Database: PDB / ID: 3dok
TitleCrystal structure of K103N mutant HIV-1 reverse transcriptase in complex with GW678248.
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE / AIDS / NNRTI / GW678248 / DRUG RESISTANCE / Hydrolase
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 / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / DNA integration / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / 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 / identical protein 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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-GWJ / PHOSPHATE ION / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChamberlain, P.P. / Ren, J. / Stammers, D.K.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Structural basis for the improved drug resistance profile of new generation benzophenone non-nucleoside HIV-1 reverse transcriptase inhibitors.
Authors: Ren, J. / Chamberlain, P.P. / Stamp, A. / Short, S.A. / Weaver, K.L. / Romines, K.R. / Hazen, R. / Freeman, A. / Ferris, R.G. / Andrews, C.W. / Boone, L. / Chan, J.H. / Stammers, D.K.
History
DepositionJul 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)116,5774
Polymers115,9642
Non-polymers6132
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-32 kcal/mol
Surface area45050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.940, 109.770, 72.480
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 / p66 RT


Mass: 64579.871 Da / Num. of mol.: 1 / Fragment: GAG-POL POLYPROTEIN P66 SUBUNIT / Mutation: K103N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: HXB2 ISOLATE / Gene: gag-pol / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HXB2
References: UniProt: P04585, UniProt: A7YKL0*PLUS, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: Protein p51 RT


Mass: 51383.969 Da / Num. of mol.: 1 / Fragment: GAG-POL POLYPROTEIN P51 SUBUNIT / Mutation: K103N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: HXB2 ISOLATE / Gene: gag-pol / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DG2 / References: UniProt: P04585
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GWJ / 2-{4-chloro-2-[(3-chloro-5-cyanophenyl)carbonyl]phenoxy}-N-(2-methyl-4-sulfamoylphenyl)acetamide


Mass: 518.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H17Cl2N3O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.63 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.933
SYNCHROTRONESRF ID14-220.933
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 30, 2001
ADSC QUANTUM 42CCDSep 30, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 24821 / % possible obs: 99.9 % / Observed criterion σ(I): -1.5 / Redundancy: 8.1 % / Biso Wilson estimate: 87.1 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 8 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2443 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DLE

3dle


Resolution: 2.9→29.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1573805.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: DUE TO THE LOW RATIO BETWEEN THE NUMBER OF REFLECTIONS AND THE NUMBER OF PARAMETERS TO BE REFINED, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 20 ANGSTROM FROM THE CA ...Details: DUE TO THE LOW RATIO BETWEEN THE NUMBER OF REFLECTIONS AND THE NUMBER OF PARAMETERS TO BE REFINED, ATOMS DISTANT FROM THE NNI-BINDING SITE (DEFINED AS ATOMS MORE THAN 20 ANGSTROM FROM THE CA ATOM OF TYR188) WERE harmonically restrained during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1203 4.9 %RANDOM
Rwork0.218 ---
obs0.218 24771 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0851 Å2 / ksol: 0.295821 e/Å3
Displacement parametersBiso mean: 75.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.43 Å20 Å20 Å2
2---13.42 Å20 Å2
3---16.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.38 Å
Luzzati d res low-30 Å
Luzzati sigma a0.46 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7703 0 39 8 7750
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.145
X-RAY DIFFRACTIONc_mcangle_it10.538
X-RAY DIFFRACTIONc_scbond_it12.628
X-RAY DIFFRACTIONc_scangle_it16.0312
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.489 104 4.4 %
Rwork0.403 2274 -
obs--97 %
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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