[English] 日本語
Yorodumi
- PDB-5jur: PB2 bound to an azaindole inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jur
TitlePB2 bound to an azaindole inhibitor
ComponentsPolymerase basic protein 2
KeywordsRNA BINDING PROTEIN / flu / polymerase / nucleotide binding / inhibitor
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
Chem-6NS / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.93 Å
AuthorsJacobs, M.D.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Discovery of Novel, Orally Bioavailable beta-Amino Acid Azaindole Inhibitors of Influenza PB2.
Authors: Farmer, L.J. / Clark, M.P. / Boyd, M.J. / Perola, E. / Jones, S.M. / Tsai, A. / Jacobs, M.D. / Bandarage, U.K. / Ledeboer, M.W. / Wang, T. / Deng, H. / Ledford, B. / Gu, W. / Duffy, J.P. / ...Authors: Farmer, L.J. / Clark, M.P. / Boyd, M.J. / Perola, E. / Jones, S.M. / Tsai, A. / Jacobs, M.D. / Bandarage, U.K. / Ledeboer, M.W. / Wang, T. / Deng, H. / Ledford, B. / Gu, W. / Duffy, J.P. / Bethiel, R.S. / Shannon, D. / Byrn, R.A. / Leeman, J.R. / Rijnbrand, R. / Bennett, H.B. / O'Brien, C. / Memmott, C. / Nti-Addae, K. / Bennani, Y.L. / Charifson, P.S.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5502
Polymers19,1741
Non-polymers3751
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.180, 81.180, 54.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 19174.324 Da / Num. of mol.: 1 / Fragment: UNP residues 318-483 / Mutation: R89K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Beijing/39/1975 H3N2 / Gene: PB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q30NP1
#2: Chemical ChemComp-6NS / (3~{R})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]-4,4-dimethyl-pentanoic acid


Mass: 375.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19F2N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.45 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well ...Details: 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well solution (1.5 M sodium formate, 100 mM sodium citrate, pH 4.7, 10 mM dithiothreitol) suspended over 1 mL of well solution, crystals transferred to a soaking solution (3.25 M sodium formate, 100 mM sodium citrate, pH 4.7) containing 1 mM inhibitor, incubated approximately 15 hours at room temperature, and then transferred to a cryo-preservative solution (soaking solution with 25% v/v glycerol) prior to freezing in liquid nitrogen

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.801→32.551 Å / Num. obs: 5006 / % possible obs: 97.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 78.25 Å2 / Rsym value: 0.067 / Net I/av σ(I): 10.59 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.802-2.954.60.6071.31100
2.95-3.1350.3632.11100
3.13-3.3550.2163.51100
3.35-3.624.90.1116.7192.2
3.62-3.964.80.07110.6186.1
3.96-4.4350.04516.51100
4.43-5.1150.03321.61100
5.11-6.264.90.035211100
6.26-8.864.90.02726.5199.7
8.86-32.5514.60.01925.5197.9

-
Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
BUSTERphasing
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4NCE

4nce


Resolution: 2.93→29.53 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.299
RfactorNum. reflection% reflectionSelection details
Rfree0.198 206 4.72 %RANDOM
Rwork0.181 ---
obs0.181 4360 97.2 %-
Displacement parametersBiso max: 166.92 Å2 / Biso mean: 70.82 Å2 / Biso min: 36.46 Å2
Baniso -1Baniso -2Baniso -3
1--5.4226 Å20 Å20 Å2
2---5.4226 Å20 Å2
3---10.8452 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.93→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 27 6 1203
Biso mean--55.05 54.52 -
Num. residues----150
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d447SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes201HARMONIC5
X-RAY DIFFRACTIONt_it1219HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion161SEMIHARMONIC5
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_contact1405SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1219HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1638HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion19.02
LS refinement shellResolution: 2.93→3.28 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.225 49 3.88 %
Rwork0.201 1214 -
all-1263 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: -37.9859 Å / Origin y: 0.9439 Å / Origin z: 2.0811 Å
111213212223313233
T0.0882 Å20.0648 Å2-0.0005 Å2--0.1751 Å2-0.0041 Å2---0.2412 Å2
L2.3311 °20.5706 °21.2743 °2-8.5954 °22.8975 °2--4.0417 °2
S-0.1693 Å °0.2437 Å °0.0554 Å °-0.9822 Å °0.1526 Å °0.0731 Å °-0.6556 Å °0.2099 Å °0.0167 Å °
Refinement TLS groupSelection details: { A|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more