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- PDB-6duh: Crystal structure of HIV-1 reverse transcriptase Y181I mutant in ... -

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Basic information

Entry
Database: PDB / ID: 6duh
TitleCrystal structure of HIV-1 reverse transcriptase Y181I mutant in complex with non-nucleoside inhibitor 25a
Components
  • p51 RT
  • p66 RT
KeywordsREPLICATION / HIV-1 reverse transcriptase / 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 / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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: 2.003 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)117,16241
Polymers113,9792
Non-polymers3,18439
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-83 kcal/mol
Surface area46130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.895, 73.229, 109.383
Angle α, β, γ (deg.)90.00, 100.30, 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: 63939.223 Da / Num. of mol.: 1 / Fragment: residues 168-722 / Mutation: K172A, K173A, Y181I, 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, 641 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.86 Å3/Da / Density % sol: 57.03 %
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: 2.003→107.619 Å / Num. obs: 84642 / % possible obs: 99.08 % / Redundancy: 3.4 % / Biso Wilson estimate: 52.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03285 / Rpim(I) all: 0.02074 / Rrim(I) all: 0.03896 / Net I/σ(I): 17.01
Reflection shellResolution: 2.003→2.12 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 13637 / CC1/2: 0.499 / Rrim(I) all: 1.134 / % possible all: 99

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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: 2.003→107.619 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 4231 5 %Random selection
Rwork0.1919 ---
obs0.1935 84624 99.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.003→107.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7924 0 197 602 8723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058303
X-RAY DIFFRACTIONf_angle_d0.71911232
X-RAY DIFFRACTIONf_dihedral_angle_d7.8644950
X-RAY DIFFRACTIONf_chiral_restr0.0481202
X-RAY DIFFRACTIONf_plane_restr0.0041397
LS refinement shellResolution: 2.003→2.075 Å
RfactorNum. reflection% reflection
Rfree0.3377 --
Rwork0.319 --
obs-8439 98.98 %
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)
11.53050.4115-0.64481.7045-0.21172.160.356-0.11310.07730.4909-0.15220.2353-0.0187-0.0468-00.8275-0.05790.09250.68330.03570.483846.847-14.937870.5154
2-0.17310.39760.08260.60211.04350.88410.32560.17010.2170.2617-0.01110.1252-0.1145-0.66730.00260.7789-0.0310.02360.73690.05390.557639.8706-17.480959.1175
30.45250.0092-0.2728-0.054-0.17910.4330.1596-0.304-0.10590.110.05750.14520.12610.16390.00020.666-0.01490.0260.49960.04430.412748.7261-18.183562.0854
40.98880.0654-0.18981.17221.28853.15520.3742-0.1323-0.64870.0519-0.033-0.15440.5512-0.07490.00310.7-0.0032-0.15820.66220.05220.729158.5443-27.326345.8618
51.7687-0.64411.21291.1383-0.64982.10950.2773-0.5805-0.81750.18640.34030.73750.1739-0.63290.05490.5059-0.0684-0.05850.54370.24130.856430.4417-20.982526.9135
62.7957-1.02531.14380.7768-0.39451.00030.04360.0159-0.10310.00080.08090.06380.123-0.102500.3735-0.03380.03460.4141-0.02230.447123.45651.56637.0282
73.37871.00740.79111.8083-0.26022.3275-0.0682-0.2192-0.05110.1450.09750.2836-0.2075-0.3413-0.00010.36540.03780.05160.54590.03110.491514.27879.05756.7139
83.1765-0.05751.38653.4922-0.53442.1521-0.10810.12620.13060.2948-0.0272-0.0626-0.09090.3103-0.00030.4732-0.02320.00270.43280.02270.346456.55752.052136.7256
90.17-0.394-0.21170.42970.24910.1557-0.55730.16980.28440.17360.13380.2653-0.11690.0346-0.00190.9128-0.1596-0.09210.54230.10740.756355.417627.185133.5585
101.8271-0.97951.48641.8082-0.29892.4997-0.25660.27560.26630.51710.0669-0.6729-0.2820.7475-0.08270.3844-0.2389-0.07920.57140.02290.50364.282514.592632.2479
110.0576-0.24370.6503-0.2326-0.11530.3071-0.29530.34820.18910.13330.0077-0.3561-0.54770.5267-0.00920.5166-0.1216-0.12410.80640.11370.676848.92322.47849.3085
122.30650.67831.21982.099-0.16342.7463-0.29190.14830.44340.23710.0187-0.0149-0.4032-0.0007-0.00040.4196-0.03870.03930.3422-0.01970.381932.285825.26918.5049
131.88610.71320.76492.74710.42942.241-0.03770.08330.16580.0673-0.076-0.0771-0.1040.02250.00010.4698-0.02790.02840.42110.00880.469243.228610.690420.2421
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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