[English] 日本語
Yorodumi
- PDB-4yd0: Influenza polymerase basic protein 2 (PB2) bound to an azaindole-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yd0
TitleInfluenza polymerase basic protein 2 (PB2) bound to an azaindole-tetrazole inhibitor
ComponentsPolymerase basic protein 2
KeywordsTRANSCRIPTION/INHIBITOR / small-molecule drug / inhibitor / flu / m7-GTP pocket / TRANSCRIPTION-INHIBITOR complex
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-4EW / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.62 Å
AuthorsJacobs, M.D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Isosteric replacements of the carboxylic acid of drug candidate VX-787: Effect of charge on antiviral potency and kinase activity of azaindole-based influenza PB2 inhibitors.
Authors: Boyd, M.J. / Bandarage, U.K. / Bennett, H. / Byrn, R.R. / Davies, I. / Gu, W. / Jacobs, M. / Ledeboer, M.W. / Ledford, B. / Leeman, J.R. / Perola, E. / Wang, T. / Bennani, Y. / Clark, M.P. / Charifson, P.S.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

-
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)19,6142
Polymers19,1741
Non-polymers4401
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.789, 80.789, 54.256
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: cap-binding domain (UNP residues 318-483)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Beijing/39/1975 H3N2 / Gene: PB2 / Plasmid: pET28b.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q30NP1
#2: Chemical ChemComp-4EW / 2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoro-N-[(1R,2S,3S,4R)-3-(1H-tetrazol-5-yl)bicyclo[2.2.2]oct-2-yl]pyrimidin-4-amine


Mass: 439.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19ClFN9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
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: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2011
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.616→25.293 Å / Num. obs: 6117 / % possible obs: 98.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 74.73 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 26.7 / Num. measured all: 28650
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 % / Rejects: _

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique all% possible all
2.616-2.6250.3742286289.9
11.729-25.2930.0172406597

-
Processing

Software
NameVersionClassification
PROCESSdata scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
PROCESSdata reduction
BUSTER-TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.62→25.29 Å / Cor.coef. Fo:Fc: 0.9526 / Cor.coef. Fo:Fc free: 0.9323 / SU R Cruickshank DPI: 0.628 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.731 / SU Rfree Blow DPI: 0.268 / SU Rfree Cruickshank DPI: 0.268
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 304 5 %RANDOM
Rwork0.1617 ---
obs0.1644 6084 98.77 %-
Displacement parametersBiso max: 153.37 Å2 / Biso mean: 71.85 Å2 / Biso min: 38.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.4624 Å20 Å20 Å2
2--1.4624 Å20 Å2
3----2.9248 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: final / Resolution: 2.62→25.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 31 72 1363
Biso mean--92.93 72.33 -
Num. residues----161
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d479SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes192HARMONIC5
X-RAY DIFFRACTIONt_it1317HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion172SEMIHARMONIC5
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_contact1604SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1317HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg1770HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion19.96
LS refinement shellResolution: 2.62→2.93 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2609 96 5.7 %
Rwork0.1895 1589 -
all0.1937 1685 -
obs--98.77 %
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)
10.07790.6312-0.4564.80613.09743.9115-0.1230.0950.1558-0.3623-0.11430.7006-0.1841-0.33030.23730.10450.1181-0.0919-0.0671-0.04830.0051-45.1453-2.98921.2198
22.8711.99860.50627.28443.65294.006-0.10970.214-0.259-0.21520.111-0.3451-0.06710.3341-0.00130.10860.09840.0373-0.1193-0.0204-0.1448-35.528-1.62183.8277
35.61411.33791.917110.76082.50035.6279-0.07790.194-0.1676-0.30880.3159-0.6739-0.18970.5189-0.2380.11510.13250.0625-0.0311-0.1167-0.0918-32.12792.52233.8106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|21 - 75}A21 - 75
2X-RAY DIFFRACTION2{A|76 - 122}A76 - 122
3X-RAY DIFFRACTION3{A|123 - 183}A123 - 183

+
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