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- PDB-4i2p: Crystal structure of HIV-1 reverse transcriptase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4i2p
TitleCrystal structure of HIV-1 reverse transcriptase in complex with rilpivirine (TMC278) based analogue
Components(Gag-Pol polyprotein) x 2
KeywordsHYDROLASE / TRANSFERASE/INHIBITOR / P51/P66 / hetero dimer / NNRTI / nonnucleoside inhibitor / AIDS / HIV / DNA recombination / RNA-directed DNA polymerase / DNA polymerase / endonuclease / multifunctional enzyme / transferase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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. / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / 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-G73 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2964 Å
AuthorsPatel, D. / Bauman, J.D. / Das, K. / Arnold, E.
CitationJournal: Retrovirology / Year: 2012
Title: A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants.
Authors: Johnson, B.C. / Pauly, G.T. / Rai, G. / Patel, D. / Bauman, J.D. / Baker, H.L. / Das, K. / Schneider, J.P. / Maloney, D.J. / Arnold, E. / Thomas, C.J. / Hughes, S.H.
History
DepositionNov 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag-Pol polyprotein
B: Gag-Pol polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4403
Polymers114,0292
Non-polymers4111
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-27 kcal/mol
Surface area46710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.650, 72.988, 109.599
Angle α, β, γ (deg.)90.00, 100.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gag-Pol polyprotein / Reverse transcriptase/ribonuclease H / Exoribonuclease H


Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: p66 (UNP Residues 600-1154) / Mutation: C879S, K771A, K772A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein Gag-Pol polyprotein / p51 RT


Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: p51 (UNP Residues 600-1077) / Mutation: C879S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#3: Chemical ChemComp-G73 / (2E)-3-[4-({6-[(4-methoxyphenyl)amino]-7H-purin-2-yl}amino)-3,5-dimethylphenyl]prop-2-enenitrile


Mass: 411.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N7O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 50 mM imidazole pH 6.6, 100 mM ammonium sulfate, 15 mM manganese sulfate, 10 mM spermine, 5 mM TCEP, 11% (w/w) PEG 8000, and 5% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.296→107.73 Å / Num. obs: 55926

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2964→41.294 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 2000 3.58 %Random
Rwork0.2159 ---
obs0.2175 55926 98.81 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.058 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3086 Å2-0 Å2-2.6254 Å2
2--1.3432 Å20 Å2
3---0.9654 Å2
Refinement stepCycle: LAST / Resolution: 2.2964→41.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7918 0 31 300 8249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058168
X-RAY DIFFRACTIONf_angle_d0.85811101
X-RAY DIFFRACTIONf_dihedral_angle_d15.7733096
X-RAY DIFFRACTIONf_chiral_restr0.061199
X-RAY DIFFRACTIONf_plane_restr0.0041395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2964-2.35380.34931310.27993557X-RAY DIFFRACTION91
2.3538-2.41740.33651380.27083715X-RAY DIFFRACTION97
2.4174-2.48850.27341420.25643804X-RAY DIFFRACTION98
2.4885-2.56880.30561420.23543849X-RAY DIFFRACTION99
2.5688-2.66060.28441420.23813822X-RAY DIFFRACTION99
2.6606-2.76710.28031440.23263876X-RAY DIFFRACTION99
2.7671-2.89310.28241440.22333869X-RAY DIFFRACTION100
2.8931-3.04550.30071440.23293894X-RAY DIFFRACTION100
3.0455-3.23630.27931440.22843863X-RAY DIFFRACTION100
3.2363-3.4860.25681440.22193911X-RAY DIFFRACTION100
3.486-3.83660.24861450.20413908X-RAY DIFFRACTION100
3.8366-4.39130.21621450.17243919X-RAY DIFFRACTION100
4.3913-5.53040.22071460.17533928X-RAY DIFFRACTION100
5.5304-41.30040.26041490.23914011X-RAY DIFFRACTION100

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