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- PDB-6x47: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 6x47
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-2-naphthonitrile (JLJ649), a Non-nucleoside Inhibitor
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
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 / 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 / establishment of integrated proviral latency / viral penetration into host nucleus / 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
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-7AX / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.767 Å
AuthorsChan, A.H. / Duong, V.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: Protein Sci. / Year: 2020
Title: Structural investigation of 2-naphthyl phenyl ether inhibitors bound to WT and Y181C reverse transcriptase highlights key features of the NNRTI binding site.
Authors: Duong, V.N. / Ippolito, J.A. / Chan, A.H. / Lee, W.G. / Spasov, K.A. / Jorgensen, W.L. / Anderson, K.S.
History
DepositionMay 22, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionJul 22, 2020ID: 5TEP
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4283
Polymers114,0292
Non-polymers3991
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-29 kcal/mol
Surface area47180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.056, 74.105, 108.429
Angle α, β, γ (deg.)90.000, 99.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: C280S, K172A, K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli BL21(DE3) (bacteria)
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 / 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 / Plasmid: PCDF-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03366
#3: Chemical ChemComp-7AX / 7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-2-naphthonitrile / JLJ649


Mass: 399.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H17N3O4 / 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: 2.83 Å3/Da / Density % sol: 56.59 % / Mosaicity: 0.587 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
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: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 32423 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 66.84 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.084 / Χ2: 2.694 / Net I/σ(I): 15.2 / Num. measured all: 111472
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.83.50.53816120.7870.3360.6351.64799.2
2.8-2.853.50.4316020.840.270.5091.68699
2.85-2.93.50.36316110.8720.2280.4291.77399.2
2.9-2.963.50.30816030.9040.1940.3651.81599.1
2.96-3.033.50.27315990.9240.1710.3231.79899.3
3.03-3.13.50.2315970.9470.1450.2731.90199.2
3.1-3.173.40.18816480.9590.1190.2232.01499.3
3.17-3.263.50.15515970.9690.0980.1842.22499.5
3.26-3.363.50.12516060.9790.0790.1482.26499.3
3.36-3.463.50.10916100.9820.0690.132.47399.4
3.46-3.593.50.09416300.9820.0590.1112.69799.5
3.59-3.733.50.08316210.9890.0530.0982.88999.6
3.73-3.93.50.07416080.9890.0470.0873.33499.6
3.9-4.113.40.06716230.9930.0420.0793.44399.6
4.11-4.363.40.06316240.9920.040.0753.62999.6
4.36-4.73.40.06316440.9920.040.0744.25999.6
4.7-5.173.40.06516370.9890.0420.0774.92699.6
5.17-5.923.40.05916460.9920.0380.073.74599.8
5.92-7.463.40.03916530.9970.0250.0462.53899.9
7.46-503.30.0416520.9940.0260.0472.87696.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TER

5ter


Resolution: 2.767→43.435 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 1620 5 %
Rwork0.234 30793 -
obs0.2357 32413 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.72 Å2 / Biso mean: 78.3541 Å2 / Biso min: 24.98 Å2
Refinement stepCycle: final / Resolution: 2.767→43.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7718 0 30 0 7748
Biso mean--69.26 --
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037962
X-RAY DIFFRACTIONf_angle_d0.63610834
X-RAY DIFFRACTIONf_chiral_restr0.0251178
X-RAY DIFFRACTIONf_plane_restr0.0031363
X-RAY DIFFRACTIONf_dihedral_angle_d11.252980
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7673-2.84880.35691250.3028238792
2.8488-2.94070.34281360.3024256399
2.9407-3.04580.35441340.3029255199
3.0458-3.16770.32051340.2861255799
3.1677-3.31180.35131360.286257399
3.3118-3.48630.31411340.2698256599
3.4863-3.70460.31891370.26072580100
3.7046-3.99050.26571360.22972581100
3.9905-4.39170.22981360.21292589100
4.3917-5.02640.21631370.20862596100
5.0264-6.32960.24381370.23012620100
6.3296-43.4350.24081380.1904263198

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