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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8djv
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 6-Bromo-3-hydroxy-N-methoxy-4-oxo-1,4-dihydropyridine-2-carboxamide
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / Drug discovery / metal-binding pharmacophore / isosteres / influenza endonuclease / VIRAL PROTEIN-INHIBITOR complex / ANTIVIRAL PROTEIN / HYDROLASE-INHIBITOR complex
Function / homologyInfluenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / viral RNA genome replication / RNA binding / : / Chem-U3U / Protein PA-X
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 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
DepositionJul 1, 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)22,7974
Polymers22,4251
Non-polymers3733
Water1,08160
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)74.465, 74.465, 120.259
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-428-

HOH

21A-454-

HOH

-
Components

#1: Protein Polymerase acidic protein / Protein PA-X


Mass: 22424.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C6Y817
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-U3U / 6-bromo-3-hydroxy-N-methoxy-4-oxo-1,4-dihydropyridine-2-carboxamide


Mass: 263.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7BrN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Aug 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.08→37.24 Å / Num. obs: 22176 / % possible obs: 99.1 % / Redundancy: 17.7 % / Biso Wilson estimate: 37.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.023 / Rrim(I) all: 0.103 / Net I/σ(I): 13
Reflection shellResolution: 2.08→2.15 Å / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1077 / CC1/2: 0.723 / Rrim(I) all: 0.815

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
APEX 2data reduction
APEX 2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6V

6e6v


Resolution: 2.08→37.23 Å / SU ML: 0.3637 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8966
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.291 2222 10.02 %
Rwork0.2626 19954 -
obs0.2654 22176 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.51 Å2
Refinement stepCycle: LAST / Resolution: 2.08→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 16 60 1557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00991528
X-RAY DIFFRACTIONf_angle_d1.20782051
X-RAY DIFFRACTIONf_chiral_restr0.0633217
X-RAY DIFFRACTIONf_plane_restr0.0095262
X-RAY DIFFRACTIONf_dihedral_angle_d19.4713577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.39781170.34951056X-RAY DIFFRACTION84.27
2.13-2.170.35381430.3541258X-RAY DIFFRACTION100
2.17-2.230.3431380.34041243X-RAY DIFFRACTION100
2.23-2.290.36581420.3231264X-RAY DIFFRACTION100
2.29-2.360.38481470.3421265X-RAY DIFFRACTION100
2.36-2.430.40771400.36151256X-RAY DIFFRACTION100
2.43-2.520.39281410.33151256X-RAY DIFFRACTION99.86
2.52-2.620.36451450.36111264X-RAY DIFFRACTION100
2.62-2.740.38791400.331249X-RAY DIFFRACTION99.93
2.74-2.880.35891450.33011262X-RAY DIFFRACTION100
2.88-3.070.32641370.30351258X-RAY DIFFRACTION100
3.07-3.30.32151370.29421256X-RAY DIFFRACTION99.71
3.3-3.630.27981420.25071261X-RAY DIFFRACTION100
3.63-4.160.23411390.20381268X-RAY DIFFRACTION99.86
4.16-5.230.21821310.1951266X-RAY DIFFRACTION99.93
5.24-37.230.22711380.21131272X-RAY DIFFRACTION99.93
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)
11.487629943821.991841574150.7224925675333.06168227481-0.4981323922955.71871003042-0.08452293892690.124343407615-0.103136364759-0.0981698317308-0.1037938883160.2636998970950.199642449620.01343489549670.1640199118310.5060540125990.1676868541330.07498279774430.564324989698-0.1596045067930.50616914956529.51162275157.09332174469-20.4139867653
24.78266870026-0.0416449924959-0.5945788489541.516527206150.6592023607122.261795544520.084084743788-0.439190847097-0.3578842857740.0942883188977-0.3337661545590.5278203168030.0990447343068-0.5074912266960.2271845221840.3042368709870.05586146006320.1055026411520.481123221311-0.08305405815470.4251849130714.844012117212.3551324658-8.37125826433
33.38449972975-0.1919038718960.5050416787253.35666517574-0.1273100106523.53307786220.165984388705-0.23574029490.4048230677060.0322585832509-0.2109240925910.179563012832-0.195908110799-0.1310468493990.04202798527590.2237641982210.04490441141440.06123094591820.371247926527-0.0322956622230.34986159741927.147712749819.2622410959-5.64143597868
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 198 )127 - 198109 - 180

+
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