[English] 日本語
Yorodumi
- PDB-6wj4: The crystal structure of the 2009/H1N1/California PA endonuclease... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wj4
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease wild type in complex with SJ000986448
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE
Function / homology
Function and homology information


viral RNA genome replication / RNA binding / metal ion binding
Similarity search - Function
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
: / Hexa Vinylpyrrolidone K15 / Chem-U3A / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W.
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.
Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W.
History
DepositionApr 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)24,5547
Polymers23,1481
Non-polymers1,4056
Water52229
1
A: Polymerase acidic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)196,42956
Polymers185,1878
Non-polymers11,24248
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation6_545x,-y-1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_445-y-1,-x-1,-z1
Buried area18230 Å2
ΔGint-337 kcal/mol
Surface area59780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.090, 90.090, 132.141
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Polymerase acidic protein


Mass: 23148.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus, (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1))
Gene: PA-X, PA / Strain: A/Luxembourg/43/2009(H1N1) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A481PFF5, UniProt: C6H0Y9

-
Non-polymers , 5 types, 35 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-U3A / 5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-3,6-dihydropyrimidine-4-carboxamide


Mass: 434.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F3N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-QQ4 / Hexa Vinylpyrrolidone K15 / 1,1',1'',1''',1'''',1'''''-[(3R,5R,7R,9S,11R)-dodecane-1,3,5,7,9,11-hexayl]hexa(pyrrolidin-2-one)


Mass: 668.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56N6O6
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 10 MM MNCL2, 10 MM MGCL2, 0.5% PVP K15

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.7 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.55→74.44 Å / Num. obs: 9099 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 55.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.023 / Rrim(I) all: 0.065 / Χ2: 0.4 / Net I/σ(I): 16.1
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1072 / CC1/2: 0.879 / Rpim(I) all: 0.329 / Rrim(I) all: 0.911 / Χ2: 0.38 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.55→63.7 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.03
RfactorNum. reflection% reflection
Rfree0.2732 443 4.87 %
Rwork0.2282 --
obs0.2305 9095 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.57 Å2 / Biso mean: 82.2965 Å2 / Biso min: 41.92 Å2
Refinement stepCycle: final / Resolution: 2.55→63.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 77 29 1515
Biso mean--124.4 70.88 -
Num. residues----179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.920.42571310.33032794292598
2.92-3.680.31491490.26212859300899
3.68-63.70.23951630.1992999316299
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)
17.73892.9743-1.70554.31392.78354.115-0.238-0.15330.65141.63790.70710.89530.19050.8499-0.67230.8658-0.0532-0.07010.90660.14530.7441-23.849-29.011-3.384
29.77521.64452.67377.55264.20382.7933-0.141-0.2127-0.64210.77120.1006-0.46881.05861.1380.17810.59610.0547-0.02250.82270.23870.644-18.097-39.877-4.335
32.4469-0.35993.72334.62162.53427.8069-0.02850.06650.31580.3203-0.2610.12960.7191-0.12360.150.567-0.0880.1650.72340.26010.6986-25.335-41.444-16.459
48.2890.53943.55156.75362.27032.3386-0.5550.2643-0.3231-0.39660.486-1.01210.47071.67070.09490.79010.07730.27510.80420.13890.7656-19.053-56.763-18.855
50.96870.02880.18192.06310.85542.63090.01630.5075-0.007-0.8672-0.3292-0.27660.0390.08680.1820.6461-0.04420.23420.63880.15010.7349-19.347-45.27-24.884
69.5171-6.52740.42218.90663.12986.05370.4658-0.69650.7743-0.453-0.1308-1.07620.5833-0.1758-0.30460.77-0.27450.23781.66460.10510.8065-10.933-35.659-27.139
73.599-0.6244-1.61768.16333.18757.2841-0.10640.33970.1924-0.3157-0.0747-0.1355-0.30090.40140.11570.4437-0.12070.01890.64210.32680.563-22.399-30.624-22.147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -2:10 )A-2 - 10
2X-RAY DIFFRACTION2( CHAIN A AND RESID 11:31 )A11 - 31
3X-RAY DIFFRACTION3( CHAIN A AND RESID 32:53 )A32 - 53
4X-RAY DIFFRACTION4( CHAIN A AND RESID 73:79 )A73 - 79
5X-RAY DIFFRACTION5( CHAIN A AND RESID 80:107 )A80 - 107
6X-RAY DIFFRACTION6( CHAIN A AND RESID 108:119 )A108 - 119
7X-RAY DIFFRACTION7( CHAIN A AND RESID 120:176 )A120 - 176

+
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