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- PDB-6duf: Crystal structure of HIV-1 reverse transcriptase V106A/F227L muta... -

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Basic information

Entry
Database: PDB / ID: 6duf
TitleCrystal structure of HIV-1 reverse transcriptase V106A/F227L 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 / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...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 / establishment of integrated proviral latency / viral penetration into host nucleus / 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 / 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. / 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: 1.963 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)116,62632
Polymers113,9672
Non-polymers2,65930
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-130 kcal/mol
Surface area45660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.061, 72.955, 108.989
Angle α, β, γ (deg.)90.00, 100.08, 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: 63927.168 Da / Num. of mol.: 1 / Fragment: residues 600-1154 / Mutation: V106A, K172A, K173A, F227L, 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, 594 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.: 18 / 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.: 564 / 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: 56 %
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: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.963→54.68 Å / Num. obs: 87349 / % possible obs: 97.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 52.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03545 / Rpim(I) all: 0.02196 / Rsym value: 0.04182 / Net I/σ(I): 15.3
Reflection shellResolution: 1.963→2.08 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 13969 / CC1/2: 0.43 / Rrim(I) all: 1.307 / % possible all: 96.6

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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: 1.963→54.68 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 4365 5 %Random selection
Rwork0.1837 ---
obs0.1859 87321 97.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.963→54.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7922 0 162 565 8649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128304
X-RAY DIFFRACTIONf_angle_d1.07511258
X-RAY DIFFRACTIONf_dihedral_angle_d6.7557004
X-RAY DIFFRACTIONf_chiral_restr0.0661205
X-RAY DIFFRACTIONf_plane_restr0.0071404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9629-1.98520.3621390.3352650X-RAY DIFFRACTION93
1.9852-2.00850.34921420.32042689X-RAY DIFFRACTION97
2.0085-2.0330.30581470.30142782X-RAY DIFFRACTION98
2.033-2.05880.31871450.2922754X-RAY DIFFRACTION98
2.0588-2.08590.31681450.27362755X-RAY DIFFRACTION98
2.0859-2.11440.27181450.25952761X-RAY DIFFRACTION98
2.1144-2.14470.31181450.2562758X-RAY DIFFRACTION98
2.1447-2.17670.29921430.24882739X-RAY DIFFRACTION98
2.1767-2.21070.29171460.24432774X-RAY DIFFRACTION98
2.2107-2.24690.28051440.2312725X-RAY DIFFRACTION97
2.2469-2.28570.29321440.22832742X-RAY DIFFRACTION97
2.2857-2.32720.24331410.22082672X-RAY DIFFRACTION95
2.3272-2.3720.25041460.21922772X-RAY DIFFRACTION98
2.372-2.42040.27961470.21442802X-RAY DIFFRACTION98
2.4204-2.4730.26551480.20812815X-RAY DIFFRACTION99
2.473-2.53060.25531470.19862793X-RAY DIFFRACTION98
2.5306-2.59390.26591460.19562767X-RAY DIFFRACTION98
2.5939-2.6640.24521460.19412778X-RAY DIFFRACTION99
2.664-2.74240.27321470.1922784X-RAY DIFFRACTION99
2.7424-2.83090.23911460.18942780X-RAY DIFFRACTION99
2.8309-2.93210.22171470.18342803X-RAY DIFFRACTION98
2.9321-3.04940.26391490.18892813X-RAY DIFFRACTION98
3.0494-3.18820.24391450.1852762X-RAY DIFFRACTION98
3.1882-3.35630.20991360.18382594X-RAY DIFFRACTION91
3.3563-3.56650.22031480.18142808X-RAY DIFFRACTION98
3.5665-3.84180.23921490.16582836X-RAY DIFFRACTION99
3.8418-4.22830.2021490.15462829X-RAY DIFFRACTION99
4.2283-4.83980.18871490.15242823X-RAY DIFFRACTION99
4.8398-6.09640.2271470.17832801X-RAY DIFFRACTION97
6.0964-54.70180.19371470.17882795X-RAY DIFFRACTION95
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)
10.52470.6256-1.01610.1520.20242.4830.358-0.25970.02740.5102-0.13620.3717-0.0248-0.0632-0.19540.9829-0.01960.15090.60530.06830.517745.9586-16.904764.4392
21.35850.68751.66781.36041.06012.37620.4169-0.4548-0.4470.46660.11180.25520.4223-0.4987-0.56090.6854-0.0560.00540.67570.2320.69942.8786-24.863940.9081
32.7223-1.2221.21361.1283-0.60350.9347-0.0023-0.2795-0.42990.09210.23520.39790.0709-0.2926-0.19930.3392-0.03370.03530.420.02480.4624.3773-3.346711.7328
43.5956-0.36260.84174.3050.06462.84030.0025-0.13670.15480.4318-0.1039-0.1353-0.19490.32370.06930.5079-0.0518-0.00640.49640.01880.358156.58342.181536.5611
51.4538-0.05480.18273.0135-1.1690.7467-0.48920.41260.85810.18860.2005-0.0774-0.45760.50270.10330.8857-0.2468-0.13240.80.13880.872558.783322.820831.6573
62.3975-0.62750.40232.1795-0.33121.54140.0779-0.42930.45340.6112-0.2313-0.4494-0.22370.43790.03210.7048-0.1723-0.10180.6035-0.01640.491160.9329.053939.1798
72.14560.7515-0.571.93280.9632.7042-0.38891.6160.4976-0.84330.5162-0.6423-0.16851.1348-0.10660.8477-0.3377-0.01281.28160.14421.043266.135722.152621.2841
81.7201-0.74381.54932.5259-1.53433.0968-0.21760.1070.27240.3529-0.1162-0.2247-0.36370.09080.30580.3464-0.0580.05150.3463-0.01750.359536.083420.001812.2639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 146 )
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 296 )
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 554 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 83 )
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 117 )
6X-RAY DIFFRACTION6chain 'B' and (resid 118 through 174 )
7X-RAY DIFFRACTION7chain 'B' and (resid 175 through 240 )
8X-RAY DIFFRACTION8chain 'B' and (resid 241 through 428 )

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