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- PDB-1ikv: K103N Mutant HIV-1 Reverse Transcriptase in Complex with Efivarenz -

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Basic information

Entry
Database: PDB / ID: 1ikv
TitleK103N Mutant HIV-1 Reverse Transcriptase in Complex with Efivarenz
Components(POL POLYPROTEIN) x 2
KeywordsTRANSFERASE / Heterodimer / protein-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-EFZ / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLindberg, J. / Unge, T.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Structural basis for the inhibitory efficacy of efavirenz (DMP-266), MSC194 and PNU142721 towards the HIV-1 RT K103N mutant.
Authors: Lindberg, J. / Sigurdsson, S. / Lowgren, S. / Andersson, H.O. / Sahlberg, C. / Noreen, R. / Fridborg, K. / Zhang, H. / Unge, T.
History
DepositionMay 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Atomic model
Revision 1.4Jul 18, 2012Group: Non-polymer description
Revision 1.5Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.7Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POL POLYPROTEIN
B: POL POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7293
Polymers114,4132
Non-polymers3161
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-29 kcal/mol
Surface area45200 Å2
MethodPISA
2
A: POL POLYPROTEIN
B: POL POLYPROTEIN
hetero molecules

A: POL POLYPROTEIN
B: POL POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,4586
Polymers228,8274
Non-polymers6312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y,-z+5/21
Buried area16090 Å2
ΔGint-78 kcal/mol
Surface area85800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.633, 157.168, 156.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a heterodimer

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Components

#1: Protein POL POLYPROTEIN / reverse transcriptase


Mass: 64500.965 Da / Num. of mol.: 1 / Mutation: K103N, E478Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: BH10 / Plasmid: PETd / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein POL POLYPROTEIN / reverse transcriptase


Mass: 49912.344 Da / Num. of mol.: 1 / Mutation: K103N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: BH10 / Plasmid: PETd / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-EFZ / (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE / DMP-266 / Efavirenz


Mass: 315.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9ClF3NO2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: ammonium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
230 mMDMSO1drop
31.4 Mammonium sulfate1reservoir
450 mMHEPES1reservoirpH7.2
55 mM1reservoirMgCl2
6300 mM1reservoirKCl

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Data collection

DiffractionMean temperature: 270 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0232 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 2000 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0232 Å / Relative weight: 1
ReflectionResolution: 3→24.84 Å / Num. all: 29822 / Num. obs: 29152 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 52.6 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 4.1
Reflection shellResolution: 3→24.84 Å / Redundancy: 2 % / Rmerge(I) obs: 0.63 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 48782
Reflection shell
*PLUS
Lowest resolution: 3.11 Å / % possible obs: 97.8 % / Num. unique obs: 2856

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24.84 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2624691.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1309 5 %RANDOM
Rwork0.228 ---
all-33010 --
obs-25992 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.43 Å2 / ksol: 0.251 e/Å3
Displacement parametersBiso mean: 52.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.7 Å20 Å20 Å2
2--1.14 Å20 Å2
3---6.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7851 0 21 0 7872
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it2.151.5
X-RAY DIFFRACTIONc_mcangle_it3.662
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 197 4.7 %
Rwork0.348 4034 -
obs-4034 86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMSUS.TOP
X-RAY DIFFRACTION3SUS.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
X-RAY DIFFRACTIONc_mcbond_it2.151.5
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_mcangle_it3.662
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.401 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.348

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