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- PDB-5ter: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Entry
Database: PDB / ID: 5ter
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 5-chloro-7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-8-methyl-2-naphthonitrile (JLJ651), a Non-nucleoside Inhibitor
Components(HIV-1 REVERSE TRANSCRIPTASE, ...) x 2
KeywordsTRANSFERASE / HYDROLASE/INHIBITOR / Polymerase / reverse transcriptase / HIV / non-nucleoside inhibitor / HYDROLASE-DNA-INHIBITOR complex / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase domain superfamily / Ribonuclease H 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-7AY / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsChan, A.H. / Anderson, K.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049551 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI044616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM032136 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI122864 United States
CitationJournal: ACS Med Chem Lett / Year: 2016
Title: Design, Conformation, and Crystallography of 2-Naphthyl Phenyl Ethers as Potent Anti-HIV Agents.
Authors: Lee, W.G. / Chan, A.H. / Spasov, K.A. / Anderson, K.S. / Jorgensen, W.L.
History
DepositionSep 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.percent_possible_all / _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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)114,5975
Polymers114,0292
Non-polymers5683
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-49 kcal/mol
Surface area46750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.620, 74.200, 108.600
Angle α, β, γ (deg.)90.000, 99.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

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HIV-1 REVERSE TRANSCRIPTASE, ... , 2 types, 2 molecules AB

#1: Protein HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT / Pr160Gag-Pol


Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: UNP residues 600-1154 / Mutation: C280S, K172A, K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Protein HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT / Pr160Gag-Pol


Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: UNP 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 (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

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Non-polymers , 4 types, 19 molecules

#3: Chemical ChemComp-7AY / 5-chloro-7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-8-methyl-2-naphthonitrile / JLJ651


Mass: 447.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H18ClN3O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM HEPES pH 7.0, 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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 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: 2.7→41.289 Å / Num. obs: 35179 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 74.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 21.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
2.7-2.773.20.4932.460.797100
2.77-2.850.3753.530.90399.8
2.85-2.930.284.920.94699.8
2.93-3.020.2016.570.97199.7
3.02-3.120.1628.120.98100
3.12-3.230.11111.090.9999.6
3.23-3.350.07715.120.995100
3.35-3.490.06218.550.996100
3.49-3.640.04822.670.99799.9
3.64-3.820.03827.570.998100
3.82-4.020.03331.520.99899.8
4.02-4.270.0334.670.99899.6
4.27-4.560.02837.450.99899.8
4.56-4.930.02738.930.99999.6
4.93-5.40.02639.50.99999.4
5.4-6.040.02938.790.99899.4
6.04-6.970.02740.130.998100
6.97-8.540.03949.880.99999.9
8.54-12.070.0356.810.99999.6
12.070.02355.110.99994

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEJun 17, 2015data scaling
PHASER1.9_1692phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSJun 17, 2015data reduction
XDSJun 17, 2015data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RW6

4rw6


Resolution: 2.7→41.289 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 30.75
RfactorNum. reflection% reflection
Rfree0.2665 1759 5 %
Rwork0.2296 --
obs0.2315 35170 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.45 Å2 / Biso mean: 85.7642 Å2 / Biso min: 30.61 Å2
Refinement stepCycle: final / Resolution: 2.7→41.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7734 0 38 16 7788
Biso mean--78.39 58.56 -
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037984
X-RAY DIFFRACTIONf_angle_d0.64210864
X-RAY DIFFRACTIONf_chiral_restr0.0251178
X-RAY DIFFRACTIONf_plane_restr0.0041367
X-RAY DIFFRACTIONf_dihedral_angle_d11.7662992
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.7730.40281330.32525362669100
2.773-2.85460.38081350.299525522687100
2.8546-2.94670.30361340.276825482682100
2.9467-3.0520.31991340.285325392673100
3.052-3.17410.34521360.281125732709100
3.1741-3.31850.30761340.277925582692100
3.3185-3.49340.29571350.260125662701100
3.4934-3.71210.32781350.253925822717100
3.7121-3.99850.28711360.234225652701100
3.9985-4.40050.25641360.215525722708100
4.4005-5.03630.20411340.205825772711100
5.0363-6.34150.29791370.223125952732100
6.3415-41.2940.20241400.18572648278899

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