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- PDB-7krd: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Entry
Database: PDB / ID: 7krd
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 4-(3-chloro-5-cyanophenoxy)-3-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenyl sulfurofluoridate (JLJ702)
Components
  • HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT
  • HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT
KeywordsTRANSFERASE / Hydrolase/Inhibitor / Polymerase / reverse transcriptase / non-nucleoside inhibitor / Hydrolase-Inhibitor complex
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
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. / 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 / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-X2S / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBertoletti, N. / Ippolito, J.A. / Jorgensen, W.L. / Anderson, K.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49551 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI155072 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Covalent Inhibition of Wild-Type HIV-1 Reverse Transcriptase Using a Fluorosulfate Warhead.
Authors: Ippolito, J.A. / Niu, H. / Bertoletti, N. / Carter, Z.J. / Jin, S. / Spasov, K.A. / Cisneros, J.A. / Valhondo, M. / Cutrona, K.J. / Anderson, K.S. / Jorgensen, W.L.
History
DepositionNov 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 18, 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: HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5113
Polymers114,0292
Non-polymers4821
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-20 kcal/mol
Surface area45400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.403, 69.471, 104.764
Angle α, β, γ (deg.)90.000, 105.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT / p66 RT


Mass: 63989.238 Da / Num. of mol.: 1
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 HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT


Mass: 50039.488 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-X2S / 4-(3-chloro-5-cyanophenoxy)-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate


Mass: 481.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H13ClFN3O7S / Feature type: SUBJECT OF INVESTIGATION
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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50 mM imidazole pH 6.5, 18% PEG 8,000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→29.232 Å / Num. obs: 42983 / % possible obs: 99.8 % / Redundancy: 6.958 % / Biso Wilson estimate: 88.795 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.08 / Χ2: 1.132 / Net I/σ(I): 17.06 / Num. measured all: 299064
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.867.161.7541.0349192689368700.6521.89299.7
2.86-3.067.1290.961.9645854643564320.8451.036100
3.06-3.36.9630.4564.1541955603360250.9550.49399.9
3.3-3.616.620.228.336686554955420.9860.23999.9
3.61-4.036.8530.10217.2434438502950250.9960.11199.9
4.03-4.647.2710.05531.1832544448344760.9990.05999.8
4.64-5.647.0380.04439.1126709379837950.9990.04899.9
5.64-7.846.4560.03544.8819427301230090.9990.03899.9
7.84-29.2326.7770.02173.53122591855180910.02297.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TW3

5tw3


Resolution: 2.7→29.232 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 2148 5 %
Rwork0.2197 40786 -
obs0.2222 42934 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 285.56 Å2 / Biso mean: 122.778 Å2 / Biso min: 55.94 Å2
Refinement stepCycle: final / Resolution: 2.7→29.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7460 0 31 0 7491
Biso mean--107.17 --
Num. residues----953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.76280.47491430.4411270199
2.7628-2.83180.43261420.3832692100
2.8318-2.90830.34621430.35032706100
2.9083-2.99380.39381410.34122699100
2.9938-3.09030.38661420.31222683100
3.0903-3.20060.28021410.2712678100
3.2006-3.32860.31191440.25822734100
3.3286-3.47990.28711430.26822717100
3.4799-3.6630.36221420.2582706100
3.663-3.8920.27161430.22852722100
3.892-4.19170.30641430.21382710100
4.1917-4.61210.2261430.1872722100
4.6121-5.27610.21911440.18682734100
5.2761-6.63450.2791460.22022759100
6.6345-29.2320.21031480.17232823100
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)
12.68880.34220.14172.8266-1.8922.2533-0.4063-1.07040.56291.2155-0.0987-0.18-0.23810.35150.59971.36160.4045-0.40221.5398-0.31620.8713487.0519.772137.805
23.63411.0340.1113.02770.42887.3232-0.0404-2.0116-0.41230.0362-0.2481-0.38120.31641.13210.40260.87570.3653-0.1332.116-0.04660.9556495.0052.337141.939
34.4371-1.7065-0.8480.7931.13565.0593-0.7872-0.6334-4.12451.8237-0.5587-0.47291.65341.1480.61081.40860.4560.10581.83490.77474.0946487.043-11.217149.036
44.85630.8811-0.31081.86370.34150.7552-0.4629-1.0406-0.8270.3410.1352-0.00290.70390.39890.24411.20250.41190.12891.01720.19870.7892473.421-7.991131.824
52.60960.1968-3.85472.01050.79066.33871.3229-0.2460.7678-0.0627-0.10.9431-0.14550.4509-1.14641.60460.2188-0.07061.56920.0121.8383449.7182.355153.314
64.84451.1601-1.3941.468-2.40863.4295-0.4356-0.5176-0.68730.68090.1010.21270.4973-0.18540.35971.4161-0.00210.34960.72010.07641.0719444.341-10.601131.845
78.2307-1.4019-5.81572.95882.15115.6018-0.1666-0.12480.2883-0.08910.3124-0.19350.5586-0.2214-0.17670.66-0.05250.04620.9290.14841.0164420.1958.331136.554
85.9456-1.3572-0.66946.1112-0.52975.5593-0.50930.13730.67930.68860.3231-0.1304-0.0521-0.06990.18560.7345-0.0134-0.14240.62450.02840.5749464.02914.621114.266
94.9012-1.57760.70235.9724-2.4284.9269-0.40320.17510.26030.58720.3275-0.0854-0.3536-0.09130.06260.5655-0.02190.00880.4978-0.0010.4907463.26118.137110.385
103.7148-2.44012.24376.7440.97885.88990.08090.7298-0.1433-0.62360.23940.3484-0.2323-0.8356-0.38370.9517-0.13990.01171.06270.24070.9527453.15429.87995.354
117.73484.7611-3.23653.5781-3.33724.47920.33851.58611.8059-0.14360.5941.2919-0.8306-1.4717-1.04531.36660.09160.26491.68990.42281.5543418.43629.72123.536
127.47221.5131-2.58140.6514-0.41621.86890.84390.39112.16650.66070.07380.7369-0.8493-0.7915-0.74171.0140.25710.18550.99830.32551.331426.83329.357121.492
134.8503-4.343-1.62245.0232-0.25283.0777-1.40922.2311-1.3076-1.77340.2613.2451-0.4114-2.35450.85671.0608-0.3743-0.39251.3933-0.13281.0793436.3278.92110.664
148.53472.5803-3.57193.9131-1.23595.1784-0.1720.1108-0.33490.93540.17380.12430.105-0.79020.02620.96820.04830.0040.73810.08370.7316442.80117.605118.096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:29 )A3 - 29
2X-RAY DIFFRACTION2( CHAIN A AND RESID 30:63 )A30 - 63
3X-RAY DIFFRACTION3( CHAIN A AND RESID 64:72 )A64 - 72
4X-RAY DIFFRACTION4( CHAIN A AND RESID 73:282 )A73 - 282
5X-RAY DIFFRACTION5( CHAIN A AND RESID 283:290 )A283 - 290
6X-RAY DIFFRACTION6( CHAIN A AND RESID 291:392 )A291 - 392
7X-RAY DIFFRACTION7( CHAIN A AND RESID 393:551 )A393 - 551
8X-RAY DIFFRACTION8( CHAIN B AND RESID 5:95 )B5 - 95
9X-RAY DIFFRACTION9( CHAIN B AND RESID 96:159 )B96 - 159
10X-RAY DIFFRACTION10( CHAIN B AND RESID 160:237 )B160 - 237
11X-RAY DIFFRACTION11( CHAIN B AND RESID 238:281 )B238 - 281
12X-RAY DIFFRACTION12( CHAIN B AND RESID 282:356 )B282 - 356
13X-RAY DIFFRACTION13( CHAIN B AND RESID 357:369 )B357 - 369
14X-RAY DIFFRACTION14( CHAIN B AND RESID 370:428 )B370 - 428

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