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- PDB-4ig0: HIV-1 reverse transcriptase with bound fragment at the 507 site -

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Basic information

Entry
Database: PDB / ID: 4ig0
TitleHIV-1 reverse transcriptase with bound fragment at the 507 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 / 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 / symbiont-mediated suppression of host gene expression / 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 / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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-1FG / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Feb 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: Reverse transcriptase/ribonuclease H
B: P51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1238
Polymers114,0862
Non-polymers1,0376
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-18 kcal/mol
Surface area47340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.336, 73.351, 108.793
Angle α, β, γ (deg.)90.00, 99.67, 90.00
Int Tables number5
Space group name H-MC121
DetailsHeterodimer of p66 and p51 subunits

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Components

#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
#3: Chemical ChemComp-1FG / 2-({[2-(3,4-dihydroquinolin-1(2H)-yl)-2-oxoethyl](methyl)amino}methyl)quinazolin-4(1H)-one


Mass: 362.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N4O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 56.05 %
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: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 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
21.0751
ReflectionResolution: 2.5→50 Å / Num. all: 44020 / Num. obs: 43932 / % possible obs: 99.8 % / Observed criterion σ(F): -2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 33.56
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.540.6091100
2.54-2.590.5391100
2.59-2.640.4711100
2.64-2.690.4251100
2.69-2.750.3431100
2.75-2.820.2931100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: dev_1233)model building
PHENIX(phenix.refine: dev_1233)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXdev_1233phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.141 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 2206 5.03 %2%
Rwork0.2009 ---
obs0.2032 43820 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→43.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7955 0 70 66 8091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058259
X-RAY DIFFRACTIONf_angle_d1.02711228
X-RAY DIFFRACTIONf_dihedral_angle_d14.2773140
X-RAY DIFFRACTIONf_chiral_restr0.0751208
X-RAY DIFFRACTIONf_plane_restr0.0051410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4988-2.55310.28091420.26292558X-RAY DIFFRACTION99
2.5531-2.61250.29731280.24732594X-RAY DIFFRACTION100
2.6125-2.67780.30521320.24042582X-RAY DIFFRACTION100
2.6778-2.75020.28491370.25072575X-RAY DIFFRACTION100
2.7502-2.83110.3171220.24562604X-RAY DIFFRACTION100
2.8311-2.92250.30771100.23712634X-RAY DIFFRACTION100
2.9225-3.02690.30721400.24362579X-RAY DIFFRACTION100
3.0269-3.14810.28341400.24292587X-RAY DIFFRACTION100
3.1481-3.29130.29121450.23642599X-RAY DIFFRACTION100
3.2913-3.46470.23391430.22382596X-RAY DIFFRACTION100
3.4647-3.68170.22511300.20572621X-RAY DIFFRACTION100
3.6817-3.96580.23471450.17522596X-RAY DIFFRACTION100
3.9658-4.36450.20961510.17182602X-RAY DIFFRACTION100
4.3645-4.99530.20391380.16412626X-RAY DIFFRACTION100
4.9953-6.29040.2321570.19462619X-RAY DIFFRACTION100
6.2904-43.14770.23381460.18362642X-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)
13.03321.0657-1.91211.8771-0.27823.32760.3465-0.1823-0.0390.5524-0.17470.18250.09020.0669-0.14271.1107-0.00970.06110.67010.08680.479347.9985-15.311270.1468
20.41420.2042-1.1446-0.40711.76838.3540.1954-0.0953-0.19910.08170.12760.22050.4472-0.3689-0.22590.93090.018-0.01620.67720.15320.660945.9558-18.079760.5947
33.0488-0.04632.79162.1275-0.16934.70930.6257-0.5603-1.16550.21450.23970.53970.5573-0.7816-0.83880.9005-0.0694-0.1190.69410.27540.909542.6741-25.809139.9838
43.319-1.39781.65563.5611-1.08714.040.358-0.2749-0.85370.02140.24130.57230.5428-0.2548-0.43780.4939-0.0467-0.12320.3570.00610.665835.2686-15.760417.6456
54.3249-1.28332.46142.191-0.49520.9699-0.0616-0.4393-0.17080.21060.12370.17090.0753-0.3182-0.09270.3198-0.03360.04190.53570.02030.462313.01316.74236.7134
64.4952.5779-0.96362.6193-2.65733.83810.31140.30440.7625-0.4019-0.6961.6501-1.4377-1.43170.39890.52080.1746-0.07910.7685-0.12850.860113.256317.24254.0824
76.0004-0.41270.94425.25970.60856.476-0.1158-0.4655-0.05040.68820.1101-0.1554-0.33930.3865-0.00480.5618-0.006-0.06310.44590.10840.308957.32220.370339.8159
82.9564-0.07541.62396.3035-2.18593.6145-0.24880.12010.47210.73660.0921-0.2837-0.62410.45230.0940.6395-0.1443-0.10220.55970.05150.43958.822410.238634.941
94.76723.3827-1.40538.9065-0.0526.1115-0.21060.6413-0.5166-0.38690.1994-1.62760.10262.1241-0.02320.7551-0.3795-0.09571.52270.21421.11868.591920.859622.6215
104.1420.0743.08533.5014-0.80385.2223-0.34730.21530.63590.2406-0.1599-0.0557-0.67770.1250.5650.4098-0.07350.06970.39420.03350.435732.819124.99717.579
114.0914-0.35161.64116.6310.96542.62170.1648-0.04330.10630.4572-0.28070.0786-0.12620.15230.12140.432-0.06620.07230.43350.03020.321943.532610.436520.1565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 155 )
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 296 )
4X-RAY DIFFRACTION4chain 'A' and (resid 297 through 421 )
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 527 )
6X-RAY DIFFRACTION6chain 'A' and (resid 528 through 554 )
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 167 )
9X-RAY DIFFRACTION9chain 'B' and (resid 168 through 238 )
10X-RAY DIFFRACTION10chain 'B' and (resid 239 through 363 )
11X-RAY DIFFRACTION11chain 'B' and (resid 364 through 428 )

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