[English] 日本語
Yorodumi
- PDB-8dpj: The crystal structure of wild type PA endonuclease (2009/H1N1/CAL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dpj
TitleThe crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023030
ComponentsProtein PA-X
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE
Function / homology
Function and homology information


viral translational frameshifting / 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-SE9 / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCuypers, M.G. / Slavish, J.P. / Rankovic, Z. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
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
DepositionJul 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
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
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: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5547
Polymers23,1481
Non-polymers1,4056
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.598, 89.598, 134.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Protein PA-X


Mass: 23148.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Luxembourg/43/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6H0Y9

-
Non-polymers , 5 types, 9 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-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
#4: Chemical ChemComp-SE9 / (2P)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide


Mass: 434.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F3N4O4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 3 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
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 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→74.51 Å / Num. obs: 10316 / % possible obs: 99.4 % / Redundancy: 4 % / Biso Wilson estimate: 70.49 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Net I/σ(I): 16.5
Reflection shellResolution: 2.45→2.55 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1139 / CC1/2: 0.858 / Rpim(I) all: 0.312

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DIP

8dip


Resolution: 2.45→44.8 Å / SU ML: 0.236 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.6989
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 470 4.56 %
Rwork0.2216 9836 -
obs0.224 10306 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.16 Å2
Refinement stepCycle: LAST / Resolution: 2.45→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 84 3 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511559
X-RAY DIFFRACTIONf_angle_d0.8612107
X-RAY DIFFRACTIONf_chiral_restr0.0476218
X-RAY DIFFRACTIONf_plane_restr0.0073265
X-RAY DIFFRACTIONf_dihedral_angle_d12.2535224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.80.36461540.29523225X-RAY DIFFRACTION99.5
2.8-3.530.35961650.29643237X-RAY DIFFRACTION99.56
3.53-44.80.23851510.19153374X-RAY DIFFRACTION98.13
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)
13.59582599752-0.5311516526460.5751363626041.178126723171.349991491984.925042558790.001827499262180.508778883894-0.3238611814430.0146292798867-0.27297721145-0.2342174535830.8692336908990.2577071000750.3166438197620.918868727992-0.1376602243580.356876234040.651098292844-0.09584909978560.8381802954734.417149742219.29510617083.92076825029
21.732892786492.242441118542.509623860643.51162758913.14190370317.31049845621-0.637657346655-0.182837399574-0.0674143711126-0.03945647730450.1109505077150.520976078718-0.4458523393770.9442036416420.4315226678970.615645492148-0.06297278114950.3088439979390.5588477378370.04618874056540.76460463083135.674434566222.238542343713.9511668287
37.08471265486-1.91961356907-0.1997247752312.84161502480.9709789679792.4826544335-0.0758456131695-0.708494290515-0.5890852727570.97291670731-0.308805050753-0.3841884166320.8898043556890.4450077199620.3977329039551.112935738760.01529994487830.2130989118890.8254583144650.3194855476310.76949860593551.231446956622.29612265521.8139926027
44.85560877547-3.516599565471.332425437053.04483914820.1468568322253.171345272460.182324842449-1.11896002443-1.460800312870.822583320432-0.0748131573810.638307883750.243259088514-0.6826957435850.1735929106971.02737120684-0.1257537965760.3192358592860.9063844889250.3256114804960.67382090702136.110858382317.286519630323.9070599512
57.45909092395-1.1753627014-4.820685095662.003181249861.438778270236.65795851087-0.722739692141-0.755215301331-1.72702079008-0.9321184368721.312585391182.520784078840.666355423899-0.933550490694-1.354277673961.779705859-0.09727025226980.247785137741.225545574060.3981650002651.1121670449534.279479930411.181854214627.4626204306
63.96926996308-0.243795941708-0.1170671047634.053923212121.520456238154.00552326655-0.177903858585-1.791501531-0.7107623395291.751741509470.25859116540.128581273523-0.233369860101-0.4739411951830.2047546458041.22670798546-0.1638889078710.511480462090.9554853557570.3452304185860.74096522989936.885236738920.148252597629.2348478922
71.60058271937-1.86574226377-0.3407090574143.13704734699-0.2704952083352.65684040245-0.0274073164286-0.174760431395-0.629217363913-0.179175451579-0.227597086561.86791702230.258085926277-0.909587487346-0.1942723877410.790308236934-0.3014882915180.6216381352930.890419855657-0.04868724276450.85879026379624.662921553323.105063450816.9503963718
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 -3 through 31 )-3 - 311 - 35
22chain 'A' and (resid 32 through 49 )32 - 4936 - 53
33chain 'A' and (resid 50 through 115 )50 - 11554 - 100
44chain 'A' and (resid 116 through 126 )116 - 126101 - 111
55chain 'A' and (resid 127 through 136 )127 - 136112 - 121
66chain 'A' and (resid 137 through 164 )137 - 164122 - 149
77chain 'A' and (resid 165 through 195 )165 - 195150 - 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://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