[English] 日本語
Yorodumi
- PDB-8ddb: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ddb
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 4-(benzyloxy)-6-bromo-3-hydroxypicolinic acid
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / Drug discovery / metal-binding pharmacophore / isosteres / influenza endonuclease / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
ACETATE ION / : / Chem-R6X / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKohlbrand, A.J. / Stokes, R.W. / Karges, J. / Seo, H. / Sankaran, B. / Cohen, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI149444 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Carboxylic Acid Isostere Derivatives of Hydroxypyridinones as Core Scaffolds for Influenza Endonuclease Inhibitors.
Authors: Stokes, R.W. / Kohlbrand, A.J. / Seo, H. / Sankaran, B. / Karges, J. / Cohen, S.M.
History
DepositionJun 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8666
Polymers22,3671
Non-polymers4995
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.228, 76.228, 121.608
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

21A-454-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 22367.428 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds

-
Non-polymers , 5 types, 85 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-R6X / 6-bromo-3-hydroxy-4-oxo-1,4-dihydropyridine-2-carboxylic acid


Mass: 234.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4BrNO4
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→66.05 Å / Num. obs: 21524 / % possible obs: 100 % / Redundancy: 25 % / Biso Wilson estimate: 53.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.015 / Rrim(I) all: 0.071 / Net I/av σ(I): 25.6 / Net I/σ(I): 25.6
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 1.288 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1158 / CC1/2: 0.876 / Rpim(I) all: 0.4 / Rrim(I) all: 1.314 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6V

6e6v


Resolution: 2.15→58.02 Å / SU ML: 0.284 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2406 2144 9.96 %
Rwork0.192 19380 -
obs0.1971 21524 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.49 Å2
Refinement stepCycle: LAST / Resolution: 2.15→58.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 23 80 1593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251539
X-RAY DIFFRACTIONf_angle_d0.51132065
X-RAY DIFFRACTIONf_chiral_restr0.0393216
X-RAY DIFFRACTIONf_plane_restr0.0046265
X-RAY DIFFRACTIONf_dihedral_angle_d6.8333199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.37641460.29611295X-RAY DIFFRACTION99.79
2.2-2.260.33141410.29441300X-RAY DIFFRACTION99.93
2.26-2.320.32291440.27971300X-RAY DIFFRACTION99.93
2.32-2.380.24221380.26551298X-RAY DIFFRACTION99.86
2.38-2.460.35681410.24261275X-RAY DIFFRACTION99.93
2.46-2.550.2971460.2641295X-RAY DIFFRACTION100
2.55-2.650.38571440.25121276X-RAY DIFFRACTION100
2.65-2.770.25361420.25851290X-RAY DIFFRACTION99.93
2.77-2.920.3131450.2421295X-RAY DIFFRACTION99.86
2.92-3.10.29241410.22521291X-RAY DIFFRACTION100
3.1-3.340.27931430.23081294X-RAY DIFFRACTION100
3.34-3.680.28371470.17861296X-RAY DIFFRACTION100
3.68-4.210.1971450.14921289X-RAY DIFFRACTION100
4.21-5.30.18981370.13741290X-RAY DIFFRACTION100
5.3-58.020.18081440.17831296X-RAY DIFFRACTION99.65
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)
18.783413965445.24118913870.5577762137884.2190960345-1.1493605860410.1857402891-0.2345126093141.42975361747-0.912205085236-0.9686985023030.5877368134390.4283519118150.4667388824320.177737926668-0.1853932348940.8358836868890.0741140113454-0.0168990761520.510816780142-0.1703267158780.65448364974129.53521399537.66275822061-20.432413176
26.874325023190.461431583831-1.036011099111.28071824525-0.06678280470392.365020338320.2394229009-0.140546970065-0.02896534724840.303815710289-0.09065826917970.365837878726-0.0529523045344-0.209863612515-0.1295152272610.587895262507-0.001302292203930.04994199178460.3248580750260.007761652845940.44304783711815.267480077813.0452182942-8.10126336644
37.91502014426-0.351670591880.402189351050.840556202943-0.3208245782441.463368820480.173653889945-0.3330436857610.5447484260760.293281745411-0.09716362358390.183800201117-0.16996800769-0.0549928262333-0.08492462300860.652259100731-0.03066904311190.04782342422690.321809636535-0.04358359270530.44416962749625.400035803719.9508555234-2.83078893681
49.63660066575-5.40750872981-4.994554033553.267708430272.657559678082.741436751320.3768205831680.586155799047-0.75812645861-0.00425207931588-0.2332620421730.937149836301-0.4736453995360.418290183379-0.08041611195920.6254570658520.023479711224-0.002456279186030.5682164619190.1093076506890.48577029027836.908042401619.9607610247-15.6305126722
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 31 )-1 - 311 - 33
22chain 'A' and (resid 32 through 126 )32 - 12634 - 108
33chain 'A' and (resid 127 through 184 )127 - 184109 - 166
44chain 'A' and (resid 185 through 197 )185 - 197167 - 179

+
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://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