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- PDB-4id5: HIV-1 reverse transcriptase with bound fragment at the RNase H pr... -

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Basic information

Entry
Database: PDB / ID: 4id5
TitleHIV-1 reverse transcriptase with bound fragment at the RNase H primer grip site
Components
  • P51 RT
  • Reverse transcriptase/ribonuclease H
Keywordstransferase/transferase inhibitor / RNA-DIRECTED DNA POLYMERASE / DNA POLYMERASE / ENDONUCLEASE / HYDROLASE / MULTIFUNCTIONAL ENZYME / transferase-transferase 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 / 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
1-methyl-5-phenyl-1H-pyrazole-4-carboxylic acid / Chem-T27 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBauman, J.D. / Patel, D. / Arnold, E.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-ray Crystallographic Fragment Screening.
Authors: Bauman, J.D. / Patel, D. / Dharia, C. / Fromer, M.W. / Ahmed, S. / Frenkel, Y. / Vijayan, R.S. / Eck, J.T. / Ho, W.C. / Das, K. / Shatkin, A.J. / Arnold, E.
History
DepositionDec 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Jun 17, 2015Group: Non-polymer description
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Nov 29, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_database_related.db_name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Reverse transcriptase/ribonuclease H
B: P51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,00722
Polymers114,0862
Non-polymers1,92120
Water16,015889
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint8 kcal/mol
Surface area46090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.052, 72.872, 109.153
Angle α, β, γ (deg.)90.00, 100.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-997-

HOH

21A-1101-

HOH

DetailsA heterodimer of p66 and p51 subunits

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Reverse transcriptase/ribonuclease H / EXORIBONUCLEASE H / P66 RT


Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: P66 (unp residues 600-1154) / Mutation: K771A, K772A, C879S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol, POL / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein P51 RT / Gag-Pol polyprotein


Mass: 50096.539 Da / Num. of mol.: 1 / Fragment: P51 (unp residues 600-1027) / Mutation: C879S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol, POL / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H

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Non-polymers , 5 types, 909 molecules

#3: Chemical ChemComp-T27 / 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile / Rilpivirine


Mass: 366.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N6 / Comment: medication*YM
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-1FF / 1-methyl-5-phenyl-1H-pyrazole-4-carboxylic acid


Mass: 202.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growpH: 6.7 / Details: pH 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 7, 2009
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 91491 / Num. obs: 91214 / % possible obs: 99.7 % / Observed criterion σ(F): -2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.95-1.980.5531100
1.98-2.020.4611100
2.02-2.060.3791100
2.06-2.10.3151100
2.1-2.150.2671100
2.15-2.20.2321100

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Processing

Software
NameVersionClassification
Adxvdata processing
PHENIX(phenix.refine: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.201 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 1841 2.02 %
Rwork0.1874 --
obs0.1879 90998 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→29.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7928 0 112 889 8929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088262
X-RAY DIFFRACTIONf_angle_d1.05911211
X-RAY DIFFRACTIONf_dihedral_angle_d14.5783110
X-RAY DIFFRACTIONf_chiral_restr0.0731203
X-RAY DIFFRACTIONf_plane_restr0.0051406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00270.25021360.23246833X-RAY DIFFRACTION100
2.0027-2.06160.32521290.22476860X-RAY DIFFRACTION100
2.0616-2.12820.25751410.21816817X-RAY DIFFRACTION100
2.1282-2.20420.25611370.21056852X-RAY DIFFRACTION100
2.2042-2.29240.24941530.20996845X-RAY DIFFRACTION100
2.2924-2.39670.25071490.2076853X-RAY DIFFRACTION100
2.3967-2.5230.21881540.2016853X-RAY DIFFRACTION100
2.523-2.6810.21971600.19396844X-RAY DIFFRACTION100
2.681-2.88780.21031260.19026866X-RAY DIFFRACTION100
2.8878-3.17810.22281470.18986895X-RAY DIFFRACTION100
3.1781-3.63720.18371320.17456912X-RAY DIFFRACTION100
3.6372-4.57970.17491390.15696907X-RAY DIFFRACTION100
4.5797-29.20390.18411380.18746820X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9344-0.73770.34274.2534-0.88493.76930.38210.15380.23550.3413-0.20740.2016-0.2881-0.1471-0.18560.3886-0.07690.03690.2066-0.05260.12448.8234-10.019964.9155
25.09290.3898-1.26464.5703-2.57993.53940.1747-0.5921-0.57640.1295-0.4087-0.36021.13880.26810.22830.77030.04220.03140.48720.07080.212945.5314-19.877275.1688
30.9234-0.2646-0.6228-0.07720.66983.7834-0.00670.0128-0.36560.1370.13710.09191.048-0.6083-0.17960.6828-0.06280.01480.40140.01990.328839.5272-17.232859.853
40.29010.0617-0.06280.17110.53412.55380.2441-0.1917-0.44910.23650.1122-0.00620.56190.0695-0.37060.4495-0.0052-0.05860.25060.06090.324750.1629-24.808649.802
52.08510.55521.00742.5853-1.4453.00130.1217-0.1772-0.24090.23910.25870.67720.1046-0.6443-0.21060.2203-0.00760.03830.23470.04510.354229.3487-19.162224.8113
62.9092-1.24281.49210.8882-0.78110.68030.0316-0.0862-0.0334-0.00530.03750.10710.0992-0.0947-0.0580.1347-0.00520.04390.1856-0.03950.162423.42261.27616.8876
74.65971.43180.38622.46720.15183.934-0.123-0.4111-0.09720.09190.07340.1785-0.0617-0.22490.02890.07770.04360.03520.22520.02760.212614.27138.78716.6716
84.758-1.04141.19644.9189-0.30214.3764-0.08830.10420.35430.3073-0.0368-0.2313-0.450.35590.06760.2118-0.0717-0.02290.13060.03170.143456.5171.462436.4563
95.11422.3772-3.57328.0225-2.78082.6556-0.3986-1.3121.22561.7748-0.11330.1224-1.70321.46340.32750.8932-0.3672-0.30970.45480.06750.854655.643726.141234.8097
101.7491-0.94540.84752.3318-1.39392.0412-0.20050.22670.65750.6708-0.1876-0.6837-0.70630.69070.31370.4736-0.2726-0.13130.35210.07590.430362.260712.422434.6732
114.1747-0.42072.91451.5336-0.34872.2912-0.34370.2110.17890.3869-0.1844-0.8589-0.26450.86310.54320.3728-0.1181-0.00660.94980.28090.674360.021420.311614.9137
122.04460.32652.37642.27-0.13974.8512-0.25580.02260.43340.2365-0.02410.0126-0.43520.06570.34290.192-0.06210.05930.1781-0.00470.214132.112325.28658.5566
133.1117-0.70431.31855.3515-0.60741.84560.09270.10240.15760.1556-0.2095-0.0268-0.0910.08250.10920.1689-0.03430.04750.1471-0.01370.105243.384210.36920.509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 253 )
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 383 )
6X-RAY DIFFRACTION6chain 'A' and (resid 384 through 473 )
7X-RAY DIFFRACTION7chain 'A' and (resid 474 through 554 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 83 )
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 104 )
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 194 )
11X-RAY DIFFRACTION11chain 'B' and (resid 195 through 253 )
12X-RAY DIFFRACTION12chain 'B' and (resid 254 through 363 )
13X-RAY DIFFRACTION13chain 'B' and (resid 364 through 428 )

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