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- PDB-6dug: Crystal structure of HIV-1 reverse transcriptase K101P mutant in ... -

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Basic information

Entry
Database: PDB / ID: 6dug
TitleCrystal structure of HIV-1 reverse transcriptase K101P mutant in complex with non-nucleoside inhibitor 25a
Components
  • p51 RT
  • p66 RT
KeywordsREPLICATION / non-nucleoside inhibitor
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / 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. / 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-K5C / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.225 Å
AuthorsYang, Y. / Nguyen, L.A. / Smithline, Z.B. / Steitz, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2018
Title: Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors.
Authors: Yang, Y. / Kang, D. / Nguyen, L.A. / Smithline, Z.B. / Pannecouque, C. / Zhan, P. / Liu, X. / Steitz, T.A.
History
DepositionJun 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p66 RT
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,02838
Polymers113,9972
Non-polymers3,03136
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-114 kcal/mol
Surface area46300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.041, 73.303, 109.306
Angle α, β, γ (deg.)90.00, 99.76, 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 p66 RT / Reverse transcriptase/ribonuclease H / Exoribonuclease H


Mass: 63957.176 Da / Num. of mol.: 1 / Fragment: residues 600-1154 / Mutation: K101P, K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 RT


Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: residues 600-1027 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366

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Non-polymers , 6 types, 424 molecules

#3: Chemical ChemComp-K5C / 4-({4-[(4-{4-[(E)-2-cyanoethenyl]-2,6-dimethylphenoxy}thieno[3,2-d]pyrimidin-2-yl)amino]piperidin-1-yl}methyl)benzene-1-sulfonamide


Mass: 574.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H30N6O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 50 mM MES buffer (pH 6.0-6.6), 10% (v/v) polyethylene glycol (PEG) 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 10 mM spermine
PH range: 6.0-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.225→54.998 Å / Num. obs: 61162 / % possible obs: 97.66 % / Redundancy: 3.5 % / Biso Wilson estimate: 63.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03781 / Rpim(I) all: 0.02347 / Rrim(I) all: 0.04461 / Net I/σ(I): 17.06
Reflection shellResolution: 2.225→2.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.104 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 9762 / CC1/2: 0.387 / Rrim(I) all: 1.315 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q


Resolution: 2.225→54.998 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.44
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 3057 5 %Random selection
Rwork0.1851 ---
obs0.1875 61125 97.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.225→54.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7923 0 186 388 8497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048337
X-RAY DIFFRACTIONf_angle_d0.7111294
X-RAY DIFFRACTIONf_dihedral_angle_d6.6227011
X-RAY DIFFRACTIONf_chiral_restr0.0481205
X-RAY DIFFRACTIONf_plane_restr0.0041407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2251-2.25990.36241340.32112530X-RAY DIFFRACTION95
2.2599-2.29690.29151370.2962599X-RAY DIFFRACTION96
2.2969-2.33650.3531360.28592592X-RAY DIFFRACTION97
2.3365-2.3790.32361400.26942652X-RAY DIFFRACTION98
2.379-2.42480.29921390.26612633X-RAY DIFFRACTION98
2.4248-2.47430.30691390.25122641X-RAY DIFFRACTION98
2.4743-2.52810.29971390.24952645X-RAY DIFFRACTION98
2.5281-2.58690.30081380.23832635X-RAY DIFFRACTION98
2.5869-2.65160.30161390.23282643X-RAY DIFFRACTION98
2.6516-2.72330.30841410.22482663X-RAY DIFFRACTION99
2.7233-2.80340.26871390.20792657X-RAY DIFFRACTION98
2.8034-2.89390.25821390.20332633X-RAY DIFFRACTION98
2.8939-2.99730.23291390.20012648X-RAY DIFFRACTION98
2.9973-3.11730.25641390.21452640X-RAY DIFFRACTION98
3.1173-3.25920.28661390.20822633X-RAY DIFFRACTION97
3.2592-3.4310.21731340.19592548X-RAY DIFFRACTION94
3.431-3.64590.26631410.1852668X-RAY DIFFRACTION99
3.6459-3.92730.21171400.16872664X-RAY DIFFRACTION99
3.9273-4.32240.22171410.15722691X-RAY DIFFRACTION99
4.3224-4.94750.21411420.15352687X-RAY DIFFRACTION99
4.9475-6.23190.21321400.17832652X-RAY DIFFRACTION97
6.2319-55.0150.18691420.16412714X-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)
12.19771.3249-1.52051.78640.0212.13490.3959-0.18680.23480.7253-0.19220.4122-0.08560.2077-0.20831.2034-0.06060.15450.84450.05020.63447.8228-14.989570.5851
20.10630.49430.51360.46951.16964.13420.17570.10880.16760.26980.04220.41310.4931-0.908-0.22131.1364-0.05380.11890.93150.09490.795640.6111-17.402959.3074
30.40930.07560.18650.23450.84191.96730.1109-0.2779-0.1470.35250.05960.32250.24130.242-0.19530.9717-0.02820.08990.66080.060.555349.4595-18.137262.2713
42.44630.42220.87412.84121.60695.20890.5433-0.2095-0.88110.2145-0.0255-0.06920.8065-0.1397-0.45340.9120.0119-0.21130.73250.07460.815658.9299-27.251645.8596
52.7951-0.00931.56451.7309-0.86953.01530.2782-0.8876-1.09160.42790.38310.8470.2188-0.8003-0.40310.7131-0.05310.01850.73660.27391.022630.5589-21.092426.9389
64.2496-2.06721.46581.5801-0.60650.77490.0555-0.068-0.22790.05820.11840.10830.1288-0.1139-0.16940.4496-0.03330.02070.4954-0.03040.502423.73111.54797.1524
74.92151.39230.60713.53530.04274.2392-0.1404-0.2359-0.00110.06090.13160.3771-0.268-0.2745-0.00870.3530.03560.06160.52220.05640.497414.33779.0236.7614
85.0265-0.7541.55085.69480.03163.9787-0.1260.1150.28560.4705-0.077-0.1169-0.08470.48760.14920.5547-0.0654-0.04570.50820.07480.394456.91492.015336.6982
90.12830.229-0.20283.7129-2.09211.1991-0.46870.00940.74660.68130.29670.2164-1.18840.32850.51821.2071-0.2607-0.1060.85590.03320.973455.669226.933933.1953
102.233-0.0980.75552.9951-1.33052.792-0.11070.26510.47790.45550.0299-0.4944-0.44350.83290.05240.7215-0.2943-0.09610.78620.04850.672364.574814.773431.9883
113.1028-1.18593.22890.3499-0.87472.8932-0.21810.6973-0.15690.3515-0.1165-0.2589-0.51110.90390.14050.6658-0.1602-0.12250.99320.20720.81848.868922.61129.0686
123.2127-0.41342.19213.0341-0.60813.6795-0.38830.04380.50370.43870.0681-0.0654-0.5923-0.06980.28890.4979-0.08170.06320.46070.020.479732.298925.27368.4947
133.1839-0.28961.36964.43610.09993.7348-0.0008-0.00930.1690.4477-0.1031-0.0058-0.20240.00970.0740.5437-0.03110.04120.46110.00730.48743.238110.556820.2911
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 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 226 )
5X-RAY DIFFRACTION5chain 'A' and (resid 227 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 4 through 83 )
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 104 )
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 212 )
11X-RAY DIFFRACTION11chain 'B' and (resid 213 through 253 )
12X-RAY DIFFRACTION12chain 'B' and (resid 254 through 363 )
13X-RAY DIFFRACTION13chain 'B' and (resid 364 through 428 )

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