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- PDB-4idk: HIV-1 reverse transcriptase with bound fragment at the 428 site -

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Basic information

Entry
Database: PDB / ID: 4idk
TitleHIV-1 reverse transcriptase with bound fragment at the 428 site
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
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 / 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 / symbiont-mediated suppression of host gene expression / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / 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-1FE / Chem-T27 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 12, 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_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)115,93321
Polymers114,0862
Non-polymers1,84719
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint7 kcal/mol
Surface area46110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.875, 73.072, 108.965
Angle α, β, γ (deg.)90.00, 100.48, 90.00
Int Tables number5
Space group name H-MC121
DetailsHeterodimer 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, 669 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, inhibitor*YM
#4: Chemical ChemComp-1FE / N-(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)glycinamide


Mass: 206.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N4O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 55.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 11% PEG 8000, 4% PEG 400, 50 MM IMIDAZOLE, 10 MM SPERMINE, 15 MM MGSO4, 100 MM AMMONIUM SULFATE,AND 5 MM TRIS(2-CARBOXYETHYL)PHOSPHINE, PH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.917 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2009
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9171
211
ReflectionResolution: 2.1→50 Å / Num. all: 73564 / Num. obs: 73263 / % possible obs: 99.59 % / Observed criterion σ(F): -3 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.91
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.140.723199.8
2.14-2.180.636199.8
2.18-2.220.5721100
2.22-2.260.51199.9
2.26-2.310.4361100
2.31-2.370.395199.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.934 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 3447 5.04 %
Rwork0.1817 --
obs0.1839 73105 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→42.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7929 0 108 650 8687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078263
X-RAY DIFFRACTIONf_angle_d1.1311222
X-RAY DIFFRACTIONf_dihedral_angle_d14.7283108
X-RAY DIFFRACTIONf_chiral_restr0.0861203
X-RAY DIFFRACTIONf_plane_restr0.0061405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0981-2.12570.29371320.24412503X-RAY DIFFRACTION94
2.1257-2.15480.27051360.23172673X-RAY DIFFRACTION100
2.1548-2.18560.26371240.22522680X-RAY DIFFRACTION100
2.1856-2.21820.29591510.22272698X-RAY DIFFRACTION100
2.2182-2.25290.24981350.21592634X-RAY DIFFRACTION100
2.2529-2.28980.25641410.20992642X-RAY DIFFRACTION100
2.2898-2.32930.24621450.20342658X-RAY DIFFRACTION100
2.3293-2.37170.24681420.19662669X-RAY DIFFRACTION100
2.3717-2.41730.28831230.2032678X-RAY DIFFRACTION100
2.4173-2.46660.24051410.19162689X-RAY DIFFRACTION100
2.4666-2.52020.26781600.18822630X-RAY DIFFRACTION100
2.5202-2.57890.22781360.18762653X-RAY DIFFRACTION100
2.5789-2.64330.23441380.18722657X-RAY DIFFRACTION100
2.6433-2.71480.25761270.18742699X-RAY DIFFRACTION100
2.7148-2.79470.20861540.19022683X-RAY DIFFRACTION100
2.7947-2.88490.26061400.18772637X-RAY DIFFRACTION100
2.8849-2.98790.25441260.19282708X-RAY DIFFRACTION100
2.9879-3.10750.22161450.19262680X-RAY DIFFRACTION100
3.1075-3.24890.26371420.19192668X-RAY DIFFRACTION100
3.2489-3.42020.2541430.18232679X-RAY DIFFRACTION100
3.4202-3.63430.21351670.17392667X-RAY DIFFRACTION100
3.6343-3.91480.19651510.15992675X-RAY DIFFRACTION100
3.9148-4.30840.18211350.1522694X-RAY DIFFRACTION100
4.3084-4.93110.19441460.15522703X-RAY DIFFRACTION99
4.9311-6.20960.21061540.18212697X-RAY DIFFRACTION100
6.2096-42.9430.20021540.17952763X-RAY DIFFRACTION99
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)
10.8201-0.01910.01362.2028-0.13873.08070.3186-0.1023-0.04720.2041-0.14820.2258-0.1726-0.0182-0.21860.3928-0.04210.03380.20050.00490.188848.3687-10.635765.0783
22.13680.1027-0.13311.0148-0.822.88070.0677-0.4293-0.35170.1089-0.1317-0.1650.78220.0843-0.12230.65410.02140.07840.3530.05480.296445.319-19.535174.6875
30.3247-0.03580.76170.55231.15782.41350.1309-0.1657-0.21030.32810.10810.16180.667-0.4899-0.05950.5673-0.02760.02960.29280.06780.348539.7099-17.552958.6893
4-0.20050.0680.53150.43440.61082.07790.1992-0.1289-0.22630.19570.11-0.020.38250.0214-0.24020.3934-0.0009-0.04360.26850.0250.326449.9003-24.885449.7371
51.1429-0.10080.54922.4133-0.72322.29350.0433-0.1345-0.21690.16950.23460.55050.1017-0.4808-0.07330.2132-0.0030.02680.24860.04020.313329.4229-19.234324.863
62.5422-1.21111.16891.1255-0.71070.71120.0148-0.0708-0.02730.01580.04170.08570.0761-0.0713-0.00430.129-0.01050.02270.1703-0.04270.130723.16511.38157.0579
73.16850.22370.7962.15040.03062.9223-0.0795-0.28620.09180.05130.10830.2523-0.1582-0.3262-0.01030.09720.02620.0360.2301-0.00630.197714.10099.06336.8031
84.0524-0.50310.80044.0783-0.02233.9107-0.07730.09270.27080.2646-0.0344-0.1521-0.31180.3505-0.05110.2098-0.0613-0.02060.150.03650.148656.33381.487536.4642
91.7461.5308-1.1454.4547-1.61220.87940.2271-0.36010.76320.9876-0.50330.2765-1.4051.61430.23980.7559-0.3052-0.24710.59430.0360.746755.886326.119533.4632
101.786-1.15691.0852.2764-1.25571.7123-0.26790.430.75830.5005-0.2256-0.9079-0.56940.84130.07440.4385-0.3509-0.12970.45580.15480.550964.314413.639131.9247
113.5424-0.88721.99851.3295-0.7411.4148-0.2073-0.2829-0.270.4633-0.0886-0.5802-0.25420.5230.19540.3788-0.0996-0.01230.73340.20770.553151.205220.634710.8013
122.03370.46642.3662.7842-0.06753.6977-0.2333-0.02840.47770.2796-0.10510.0153-0.4279-0.04910.31270.1968-0.08260.08260.2152-0.01690.199932.268925.00098.5672
132.8770.02510.74255.0802-0.59581.65190.13510.08790.23960.1847-0.2605-0.0917-0.09450.09590.1230.1747-0.04260.02460.1843-0.00010.134843.157210.438620.1773
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 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 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 211 )
11X-RAY DIFFRACTION11chain 'B' and (resid 212 through 253 )
12X-RAY DIFFRACTION12chain 'B' and (resid 254 through 363 )
13X-RAY DIFFRACTION13chain 'B' and (resid 364 through 428 )

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