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- PDB-4icl: HIV-1 reverse transcriptase with bound fragment at the incoming d... -

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Basic information

Entry
Database: PDB / ID: 4icl
TitleHIV-1 reverse transcriptase with bound fragment at the incoming dNTP binding 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 / 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 / Retrovirus capsid, C-terminal / 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
4-(4-methylpiperazin-1-yl)benzoic acid / Chem-T27 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 10, 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: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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)115,55616
Polymers114,0862
Non-polymers1,47014
Water12,412689
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-5 kcal/mol
Surface area46300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.053, 72.648, 109.480
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number5
Space group name H-MC121

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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, 703 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-MG / MAGNESIUM ION


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


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-14N / 4-(4-methylpiperazin-1-yl)benzoic acid


Mass: 220.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growMethod: 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, TEMPERATURE 277.0K , VAPOR ...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, TEMPERATURE 277.0K , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 20, 2008
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: 1.8→50 Å / Num. all: 119988 / Num. obs: 117469 / % possible obs: 97.9 % / Observed criterion σ(F): -2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.01
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.833.30.735184.6
1.83-1.863.50.625195.7
1.86-1.93.50.52196.5
1.9-1.943.50.403196.9
1.94-1.983.50.332197.4
1.98-2.033.50.271197.5

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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: 1.8→38 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 2123 2 %
Rwork0.1788 --
obs0.1792 114627 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7929 0 89 689 8707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148252
X-RAY DIFFRACTIONf_angle_d1.44111205
X-RAY DIFFRACTIONf_dihedral_angle_d14.683129
X-RAY DIFFRACTIONf_chiral_restr0.0841215
X-RAY DIFFRACTIONf_plane_restr0.011408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83910.30981320.29536786X-RAY DIFFRACTION96
1.8391-1.88190.27031290.27166799X-RAY DIFFRACTION96
1.8819-1.9290.26031370.24546871X-RAY DIFFRACTION97
1.929-1.98110.21241400.22816945X-RAY DIFFRACTION97
1.9811-2.03940.22081390.20756913X-RAY DIFFRACTION98
2.0394-2.10530.24281370.19566951X-RAY DIFFRACTION98
2.1053-2.18050.23521500.18887004X-RAY DIFFRACTION98
2.1805-2.26780.22621400.18147049X-RAY DIFFRACTION99
2.2678-2.3710.18891630.17817001X-RAY DIFFRACTION99
2.371-2.4960.22061620.17977094X-RAY DIFFRACTION100
2.496-2.65230.20791440.17517074X-RAY DIFFRACTION100
2.6523-2.8570.22221640.18067098X-RAY DIFFRACTION100
2.857-3.14440.22751730.1847128X-RAY DIFFRACTION100
3.1444-3.59910.19771350.17577165X-RAY DIFFRACTION100
3.5991-4.53330.15641230.15567235X-RAY DIFFRACTION100
4.5333-38.00820.16371230.16887223X-RAY DIFFRACTION98
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)
10.43730.12090.35970.38030.36671.55740.1036-0.1874-0.12940.1330.02250.13570.213-0.2073-0.13690.3216-0.02820.04620.290.05520.286343.6541-21.110352.8672
21.4862-0.04560.72291.8137-0.70332.57650.126-0.0029-0.2915-0.01180.18660.53210.2084-0.4503-0.11450.1983-0.01850.00410.19280.02870.287533.6307-19.026820.9858
32.5624-1.00461.53110.2321-0.36780.7604-0.0811-0.3121-0.12690.07440.14510.16810.0255-0.26270.00380.16270.00090.0760.27730.02540.227619.30354.66886.8146
43.0499-0.3270.81353.6842-0.36782.5568-0.07050.07750.290.1479-0.089-0.1583-0.41710.3615-0.0060.2286-0.06140.00170.19190.0330.136656.40731.47936.6419
51.7114-0.36730.62783.1134-0.98272.2537-0.28050.29580.76570.55130.0217-0.4453-0.77040.676-0.07060.455-0.2927-0.13050.34430.12220.471560.911315.088734.6602
63.5983-0.47882.58590.4653-0.28321.9788-0.0321-0.0582-0.21970.0669-0.1421-0.6096-0.24930.7581-0.00210.279-0.1702-0.05971.09370.26870.78260.171320.363115.1473
72.47970.29672.26262.47280.49485.3668-0.3630.02520.57520.13850.11810.1425-0.8854-0.06720.35480.2881-0.02110.05150.2397-0.00330.267426.817430.02185.4214
82.4419-0.11821.62614.2576-0.46682.3606-0.04080.16690.0864-0.0425-0.1615-0.0472-0.15270.07260.12990.2431-0.01710.06160.1872-0.01470.148442.915312.396218.1642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 296 )
2X-RAY DIFFRACTION2chain 'A' and (resid 297 through 383 )
3X-RAY DIFFRACTION3chain 'A' and (resid 384 through 554 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 83 )
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 194 )
6X-RAY DIFFRACTION6chain 'B' and (resid 195 through 253 )
7X-RAY DIFFRACTION7chain 'B' and (resid 254 through 325 )
8X-RAY DIFFRACTION8chain 'B' and (resid 326 through 428 )

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