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- PDB-7slr: HIV Reverse Transcriptase with compound Pyr01 -

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Basic information

Entry
Database: PDB / ID: 7slr
TitleHIV Reverse Transcriptase with compound Pyr01
ComponentsReverse transcriptase/ribonuclease H
KeywordsVIRAL PROTEIN / HIV / reverse transcriptase / RT / NNRTI
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase 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 / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
Similarity search - Function
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 ...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. / 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 / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-9QI / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.179 Å
AuthorsKlein, D.J. / Zebisch, M. / Gu, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Transl Med / Year: 2023
Title: Potent targeted activator of cell kill molecules eliminate cells expressing HIV-1.
Authors: Balibar, C.J. / Klein, D.J. / Zamlynny, B. / Diamond, T.L. / Fang, Z. / Cheney, C.A. / Kristoff, J. / Lu, M. / Bukhtiyarova, M. / Ou, Y. / Xu, M. / Ba, L. / Carroll, S.S. / El Marrouni, A. / ...Authors: Balibar, C.J. / Klein, D.J. / Zamlynny, B. / Diamond, T.L. / Fang, Z. / Cheney, C.A. / Kristoff, J. / Lu, M. / Bukhtiyarova, M. / Ou, Y. / Xu, M. / Ba, L. / Carroll, S.S. / El Marrouni, A. / Fay, J.F. / Forster, A. / Goh, S.L. / Gu, M. / Krosky, D. / Rosenbloom, D.I.S. / Sheth, P. / Wang, D. / Wu, G. / Zebisch, M. / Zhao, T. / Zuck, P. / Grobler, J. / Hazuda, D.J. / Howell, B.J. / Converso, A.
History
DepositionOct 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: Reverse transcriptase/ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8913
Polymers129,3882
Non-polymers5021
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-30 kcal/mol
Surface area44580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.427, 154.243, 155.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT


Mass: 64694.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Chemical ChemComp-9QI / 5-(difluoromethyl)-3-({1-[(5-fluoro-2-oxo-1,2-dihydropyridin-3-yl)methyl]-6-oxo-4-(1,1,2,2-tetrafluoroethyl)-1,6-dihydropyrimidin-5-yl}oxy)-2-methylbenzonitrile


Mass: 502.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H13F7N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 950 mM sodium malonate pH 7.0, 100 mM HEPES/NaOH pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.179→93.43 Å / Num. obs: 58052 / % possible obs: 78.7 % / Redundancy: 6.3 % / CC1/2: 1 / Net I/σ(I): 19
Reflection shellResolution: 2.179→2.315 Å / Num. unique obs: 2906 / CC1/2: 0.589

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (18-SEP-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.179→93.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.2 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 2853 4.91 %RANDOM
Rwork0.2004 ---
obs0.202 58052 78.7 %-
Displacement parametersBiso max: 134.41 Å2 / Biso mean: 61.8 Å2 / Biso min: 34.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.4012 Å20 Å20 Å2
2---1.7754 Å20 Å2
3---3.1767 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.179→93.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7747 0 35 256 8038
Biso mean--51.15 56.18 -
Num. residues----943
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2818SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1314HARMONIC5
X-RAY DIFFRACTIONt_it8052HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1036SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6182SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8052HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg10957HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion18.43
LS refinement shellResolution: 2.18→2.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2551 52 4.48 %
Rwork0.2118 1110 -
all0.2137 1162 -
obs--12.99 %
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)
10.279-0.31810.30920.8058-0.32251.08740.11290.0334-0.1208-0.0429-0.05960.15290.1517-0.025-0.0532-0.14360.0444-0.0209-0.1130.0109-0.01796.089929.853928.1714
20.2075-0.0216-0.36811.1023-0.12660.68750.1338-0.0614-0.0558-0.0921-0.0570.0679-0.17060.1747-0.0768-0.02560.00150.0346-0.0226-0.0033-0.051522.070755.746112.5685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 538
2X-RAY DIFFRACTION2{ B|* }B6 - 428

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