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- PDB-3ith: Crystal structure of the HIV-1 reverse transcriptase bound to a 6... -

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Basic information

Entry
Database: PDB / ID: 3ith
TitleCrystal structure of the HIV-1 reverse transcriptase bound to a 6-vinylpyrimidine inhibitor
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE / HYDROLASE / HIV-1 / inhibitor / RT
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / 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 / DNA integration / 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 / 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 / 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-EDM / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFreisz, S. / Bec, G. / Wolff, P. / Dumas, P. / Radi, M. / Botta, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Crystal Structure of HIV-1 Reverse Transcriptase Bound to a Non-Nucleoside Inhibitor with a Novel Mechanism of Action
Authors: Freisz, S. / Bec, G. / Radi, M. / Wolff, P. / Crespan, E. / Angeli, L. / Dumas, P. / Maga, G. / Botta, M. / Ennifar, E.
History
DepositionAug 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 16, 2014Group: Refinement description
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Reverse transcriptase/ribonuclease H
B: p51 RT
C: Reverse transcriptase/ribonuclease H
D: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,3416
Polymers228,8874
Non-polymers4552
Water00
1
A: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6713
Polymers114,4432
Non-polymers2271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-27 kcal/mol
Surface area45880 Å2
MethodPISA
2
C: Reverse transcriptase/ribonuclease H
D: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6713
Polymers114,4432
Non-polymers2271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-29 kcal/mol
Surface area46080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.100, 72.490, 216.290
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Reverse transcriptase/ribonuclease H / HIV-1 reverse transcriptase / p66 RT


Mass: 64516.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Strain: type 1 BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: Protein p51 RT


Mass: 49927.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Strain: type 1 BH10 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366
#3: Chemical ChemComp-EDM / 6-ethenyl-N,N-dimethyl-2-(methylsulfonyl)pyrimidin-4-amine


Mass: 227.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O2S
Sequence detailsE465Q IS MUTAGENESIS ACCORDING TO REFERENCE 9 OF DATABASE UNIPROTKB/SWISS-PROT P03366 (POL_HV1B1).

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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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 100mM Hepes, 200mM ammonium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.8→44 Å / Num. all: 136888 / Num. obs: 116796 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 79.78 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.052 / Net I/σ(I): 18.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 3.2 / Num. unique all: 7811 / Rsym value: 0.592 / % possible all: 57.1

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.4_57)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLO

1dlo


Resolution: 2.8→43.895 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.746 / SU ML: 0.32 / σ(F): 1.99 / σ(I): 0 / Phase error: 31.87 / Stereochemistry target values: ML / Details: THE FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflection
Rfree0.2697 5833 4.99 %
Rwork0.2117 --
obs0.2146 116787 85.28 %
all-136888 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.931 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 182.91 Å2 / Biso mean: 91.144 Å2 / Biso min: 40.45 Å2
Baniso -1Baniso -2Baniso -3
1-4.68 Å2-0 Å2-18.289 Å2
2---12.911 Å20 Å2
3---8.231 Å2
Refinement stepCycle: LAST / Resolution: 2.8→43.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15882 0 30 0 15912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116346
X-RAY DIFFRACTIONf_angle_d1.32822218
X-RAY DIFFRACTIONf_dihedral_angle_d21.5696144
X-RAY DIFFRACTIONf_chiral_restr0.0822410
X-RAY DIFFRACTIONf_plane_restr0.0082798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.8320.3451510.3132813296466
2.832-2.8650.3231530.2882946309967
2.865-2.90.3421550.2772986314169
2.9-2.9370.3891540.2752910306468
2.937-2.9750.361590.2763075323470
2.975-3.0160.4371690.2733185335472
3.016-3.0590.3331640.2583070323472
3.059-3.1050.321700.2513195336574
3.105-3.1530.291760.2533332350876
3.153-3.2050.3311700.2623267343776
3.205-3.260.3561790.2553441362078
3.26-3.320.2871820.2513399358179
3.32-3.3830.3581850.2493500368581
3.383-3.4530.3361910.2343632382382
3.453-3.5270.3111890.2363615380484
3.527-3.6090.2441980.2243746394487
3.609-3.70.292020.2253777397988
3.7-3.80.2482110.2174017422891
3.8-3.9110.2682120.2143995420793
3.911-4.0380.2862200.2034221444196
4.038-4.1820.2692260.1884248447499
4.182-4.3490.252230.1774247447099
4.349-4.5470.2192310.1684299453099
4.547-4.7860.2262200.1634236445698
4.786-5.0860.22250.174329455499
5.086-5.4780.2232250.1784270449599
5.478-6.0280.2392260.1874330455699
6.028-6.8970.2562240.1964278450299
6.897-8.6790.2242210.1784303452499
8.679-43.90.2492220.1974292451499

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