[English] 日本語
Yorodumi
- PDB-7n55: The crystal structure of the mutant I38T PA endonuclease (2009/H1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n55
TitleThe crystal structure of the mutant I38T PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988514
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / Hydrolase/Inhibitor / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / 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 / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / 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
Chem-09Y / : / Hexa Vinylpyrrolidone K15 / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsCuypers, M.G. / Slavish, J.P. / 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
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 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: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6809
Polymers23,1361
Non-polymers1,5438
Water28816
1
A: Polymerase acidic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)197,43772
Polymers185,0908
Non-polymers12,34764
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 area21990 Å2
ΔGint-589 kcal/mol
Surface area60030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.635, 89.635, 133.761
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 Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 23136.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds

-
Non-polymers , 5 types, 24 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#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-09Y / 5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide


Mass: 380.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 57.63 %
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-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→74.46 Å / Num. obs: 11904 / % possible obs: 99.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 54.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.02 / Χ2: 0.67 / Net I/σ(I): 20
Reflection shellResolution: 2.33→2.41 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1142 / CC1/2: 0.841

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7N47

7n47


Resolution: 2.33→46 Å / SU ML: 0.3808 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.3041
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2677 617 5.19 %
Rwork0.2263 11278 -
obs0.2284 11895 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.57 Å2
Refinement stepCycle: LAST / Resolution: 2.33→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 91 16 1538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00161553
X-RAY DIFFRACTIONf_angle_d0.45742102
X-RAY DIFFRACTIONf_chiral_restr0.0373219
X-RAY DIFFRACTIONf_plane_restr0.0028264
X-RAY DIFFRACTIONf_dihedral_angle_d14.3484224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.560.35641750.31142753X-RAY DIFFRACTION99.15
2.56-2.940.37521440.30932785X-RAY DIFFRACTION99.69
2.94-3.70.34021460.252816X-RAY DIFFRACTION99.2
3.7-460.20631520.19022924X-RAY DIFFRACTION97.62
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)
13.99124546653-1.2294166573-2.651761389862.986622033463.580095267294.8069569502-0.42231549127-0.2968017427640.1150665051.073751860780.4032386855220.05815148520090.1932968526090.5998155022380.03927390476890.59466040249-0.0899637889149-0.0762035953980.7694736965440.2318863176010.568170719969-21.7385077597-33.8926172011-4.05543076512
28.482145827750.9033031260271.326144736424.145348934232.331958500561.498499159930.5744469657430.662742892220.2471572964110.028916860584-1.01896757231-2.165147655120.04804347597050.8326200499090.4910785797350.77323318080.00868019635012-0.09692266495551.117271417010.3830679746390.904826911376-11.6249418495-36.0939694559-3.39316056751
34.841577708593.458224330333.921303805835.995706394784.795862467994.324927665230.167565429394-0.0412293348614-0.03526545329740.476593634418-0.405315405853-0.1472662348760.708472330624-0.3780148161730.1275100919810.491967003309-0.0990807110868-0.007250033039780.5974374894810.2842937942640.625282621173-22.8605992228-35.9309753549-14.2464157025
42.57687238425-0.833234806492-0.3904245837287.47518623198-0.7424644538543.14139522805-0.2760866330670.600132181365-0.232778920946-0.7930848073580.0602187326243-0.2876522684610.2645061989380.4088853905020.149061717730.586287005992-0.01025462717630.2126783023870.7941969277020.169370913940.538028340696-21.1373960144-48.3759122737-22.1812983593
58.09625855588-3.745078218760.6972002870915.457178210942.925291944772.887637099180.00520862004028-0.9902360172440.903475242312-1.578264987680.45924261484-1.18625800493-0.5947632214160.793440631023-0.8161871727590.984097519027-0.4767284045160.1896784996251.978579139540.2716711875110.964230101848-10.6830376002-34.8302646808-27.5734367377
63.098397652330.544622989027-0.3390665190228.367128417493.058956594184.613607748340.01627611598460.705562003250.329475118124-0.6912671647570.152317324449-0.540310393272-0.17122973687-0.138276099562-0.1982301555630.710191454484-0.1562563540560.1169124330020.9746325180690.2261885954630.620736293905-20.6769889882-36.6435553115-29.285909398
70.6993177323-0.8594101764790.2519508781012.776521151591.803302598162.86802967451-0.120648450489-0.2333499107840.30222974319-0.0309088736347-0.214550621163-0.0235900777838-0.6938824085960.3482070298990.1184919624930.658749437694-0.306390849862-0.1277712462930.7246820401020.3780531641560.724259005804-23.3703387362-24.8752636593-16.8177049994
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 23 )-3 - 231 - 27
22chain 'A' and (resid 24 through 31 )24 - 3128 - 35
33chain 'A' and (resid 32 through 50 )32 - 5036 - 54
44chain 'A' and (resid 51 through 126 )51 - 12655 - 111
55chain 'A' and (resid 127 through 137 )127 - 137112 - 122
66chain 'A' and (resid 138 through 164 )138 - 164123 - 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