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- PDB-8dxg: HIV-1 reverse transcriptase/rilpivirine with bound fragment 5-(tr... -

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Basic information

Entry
Database: PDB / ID: 8dxg
TitleHIV-1 reverse transcriptase/rilpivirine with bound fragment 5-(trifluoromethyl)pyridin-2-ol at W24 site
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE / HIV-1 reverse transcriptase
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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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. / 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-T27 / 5-(trifluoromethyl)pyridin-2-one / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChopra, A. / Ruiz, F.X. / Bauman, J.D. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening.
Authors: Chopra, A. / Bauman, J.D. / Ruiz, F.X. / Arnold, E.
History
DepositionAug 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)115,76020
Polymers114,0292
Non-polymers1,73118
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-59 kcal/mol
Surface area46360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.623, 73.003, 109.791
Angle α, β, γ (deg.)90.000, 100.560, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease 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 BH10
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366

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Non-polymers , 7 types, 449 molecules

#3: Chemical ChemComp-U4D / 5-(trifluoromethyl)pyridin-2-one


Mass: 163.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4F3NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-T27 / 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile / Rilpivirine / Rilpivirine


Mass: 366.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N6 / Comment: medication, inhibitor*YM
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10-12% PEG 8000, 4% PEG 400, 100 mM imidazole pH 6.4-6.6, 15 mM MgSO4, 100 mM amm sulfate, 5 mM TCEP
PH range: 6.4-6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 73464 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 34.74 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.061 / Rrim(I) all: 0.118 / Χ2: 1.132 / Net I/σ(I): 9.6 / Num. measured all: 257458
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.40.69836540.660.4310.8241.21599.8
2.14-2.183.50.60436430.7450.3690.7111.25599.8
2.18-2.223.50.53336660.7430.3250.6271.288100
2.22-2.263.40.47536400.7950.2910.5591.34199.9
2.26-2.313.50.41236450.8590.2510.4851.20699.8
2.31-2.373.30.3436360.8760.2160.4051.163100
2.37-2.423.40.30136730.9020.1870.3551.12199.9
2.42-2.493.50.26136620.9280.1570.3051.13399.8
2.49-2.563.30.22236370.9390.1390.2631.1799.9
2.56-2.653.60.18936670.9560.1130.2211.13999.9
2.65-2.743.60.16236840.9630.0970.191.19199.9
2.74-2.853.60.13836730.9660.0820.1611.14699.7
2.85-2.983.50.12436440.9710.0760.1461.21899.7
2.98-3.143.50.1136710.9630.0680.131.18399.9
3.14-3.333.50.136710.9710.0610.1171.0399.9
3.33-3.593.60.08636800.9850.0510.10.93199.8
3.59-3.953.70.07736870.9870.0450.090.97299.9
3.95-4.523.50.07237150.9860.0440.0841.00299.9
4.52-5.73.60.0737320.9880.0420.0820.99599.9
5.7-503.60.0737840.9910.0410.0811.00399.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q


Resolution: 2.1→38.09 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 3821 2.73 %
Rwork0.2013 135891 -
obs0.202 73452 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.66 Å2 / Biso mean: 49.025 Å2 / Biso min: 17.41 Å2
Refinement stepCycle: final / Resolution: 2.1→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7949 0 103 432 8484
Biso mean--59.74 44.33 -
Num. residues----971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.130.32931280.29994692482090
2.13-2.160.31751400.29515067520798
2.16-2.190.27121430.2855035517897
2.19-2.220.28991390.28725076521597
2.22-2.250.311380.28085041517997
2.25-2.290.31041430.27315084522797
2.29-2.320.2931440.26875010515497
2.32-2.360.25771420.24884962510495
2.36-2.410.27251380.25094975511395
2.41-2.450.27051420.23944979512197
2.45-2.50.26211410.24295138527997
2.5-2.560.25231340.24214863499795
2.56-2.620.24691420.23525043518596
2.62-2.680.25571440.23955083522798
2.68-2.760.27271450.23035071521698
2.76-2.840.26911430.22275031517497
2.84-2.930.21591440.21545107525197
2.93-3.030.27431400.22114954509496
3.03-3.150.26351360.21125072520897
3.15-3.30.25071460.20945032517897
3.3-3.470.22941430.19374998514196
3.47-3.690.2161450.18035114525998
3.69-3.970.21421420.16945072521498
3.97-4.370.17281450.15445047519297
4.37-50.17171440.15755092523698
5-6.30.1671450.1775131527699
6.3-38.090.18551450.16425122526798
Refinement TLS params.Method: refined / Origin x: 41.0331 Å / Origin y: -1.285 Å / Origin z: 29.2373 Å
111213212223313233
T0.1661 Å2-0.0063 Å20.0398 Å2-0.1683 Å2-0.013 Å2--0.1789 Å2
L0.4004 °2-0.1851 °20.5295 °2-0.2524 °2-0.2929 °2--0.8195 °2
S0.0098 Å °0.0333 Å °-0.0246 Å °0.0833 Å °0.0065 Å °0.0365 Å °-0.0519 Å °0.0074 Å °-0.005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 554
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allB5 - 428
4X-RAY DIFFRACTION1allR1
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allD12 - 14
7X-RAY DIFFRACTION1allY3 - 5
8X-RAY DIFFRACTION1allC1
9X-RAY DIFFRACTION1allS1 - 439
10X-RAY DIFFRACTION1allG1 - 3

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