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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7knr
TitleThe crystal structure of the I38T mutant PA endonuclease (2009/H1N1/California) in complex with SJ000988558
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-WTD / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Jayaraman, S. / White, S.W.
Citation
Journal: To Be Published
Title: The crystal structure of the I38T mutant PA endonuclease (2009/H1N1/California) in complex with SJ000988558
Authors: Cuypers, M.G. / Slavish, P.J. / Jayaraman, S. / White, S.W.
#1: Journal: 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
DepositionNov 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Oct 18, 2023Group: Refinement description / Category: 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)24,6218
Polymers23,1361
Non-polymers1,4847
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein PA-X
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)196,96564
Polymers185,0908
Non-polymers11,87456
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area21270 Å2
ΔGint-444 kcal/mol
Surface area57490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.173, 89.173, 131.846
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: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T
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 BL21(DE3) (bacteria) / References: UniProt: A0A4D6EED0, UniProt: C6H0Y9

-
Non-polymers , 5 types, 38 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-WTD / 2-(2,6-difluorophenyl)-5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide


Mass: 417.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F2N3O5 / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
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: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→45.57 Å / Num. obs: 9573 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 46.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Net I/σ(I): 18.1
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1065 / CC1/2: 0.689 / Rpim(I) all: 0.446 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.48→39.42 Å / SU ML: 0.3658 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 468 4.89 %
Rwork0.2051 9104 -
obs0.2074 9572 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.17 Å2
Refinement stepCycle: LAST / Resolution: 2.48→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 88 31 1555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461556
X-RAY DIFFRACTIONf_angle_d0.70172104
X-RAY DIFFRACTIONf_chiral_restr0.0471218
X-RAY DIFFRACTIONf_plane_restr0.0048264
X-RAY DIFFRACTIONf_dihedral_angle_d6.8686223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.840.39021170.28663039X-RAY DIFFRACTION99.09
2.84-3.580.25461650.23352998X-RAY DIFFRACTION98.26
3.58-39.420.22521860.17653067X-RAY DIFFRACTION96.39
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)
13.73247151036-1.04569746075-1.64217859795.9470487423-3.130253768168.51646847363-0.170855402758-0.1683154441880.297245930885-1.46322277050.405918458007-0.167847012505-0.1601687745-1.19403144829-0.3853656288370.7221046259530.0367232578136-0.1250432902890.697779501894-0.1765168218280.494679901527-21.187233681316.16309797743.32939893728
26.756254326490.4458449986561.218656977728.67040299128-2.940326150296.644277593740.183758871150.988591513166-0.417563127264-0.8772869214770.1418011701040.9503812828110.86995845969-0.989194176591-0.2904790573380.536543932467-0.0800361653602-0.02192856049290.741943790363-0.2279965909730.581921718571-26.91823464135.369487225464.10891728933
30.8551618109770.6674094142690.7436464879174.26788327664-1.286852314774.85435372411-0.2249129875710.114597497772-0.01797529836350.0310284441265-0.0386461441567-0.1352029619220.471730200030.1626049370660.2399724143220.4128800914890.07391407731090.07368351078010.527449027098-0.1944049231790.50778620985-19.73460052043.6425949628216.3341032202
42.89814135328-0.00831679415983-0.6012201384434.65762511604-0.9048807553893.13084372573-0.236382044752-0.4566230512770.01616033055230.548106721095-0.06590099678940.3807875301480.0911847611065-0.4149289283080.1759255301070.443363328534-0.01860264022070.1865481964720.585968303383-0.1229351583210.486112819616-25.5828061665-3.9109298273322.8264074468
55.117524461385.617672207283.008678635329.327974607010.7112069508783.870241971720.172368681856-0.06513144710710.9158658540971.193341192020.2351390645011.54987678159-0.449268772695-0.258625773611-0.505273061510.6360304371020.1622586910730.1779651359051.53249634102-0.2348204689540.719482523818-33.89672985568.8066422264226.9659050277
63.161669752990.309206663713-0.4639227675587.37011244734-4.35892882457.6406802882-0.153999682602-0.6504271923520.2371864564731.20810723651-0.06360309279930.295669906813-0.1119521482410.4685343112270.2448680691150.5291106808720.1559475691920.1167370747360.665071820213-0.2270607148250.493836780814-23.86048819948.0631465939829.2602395346
70.8944812189111.15960001912-0.2542729971871.61915585315-1.06903278413.24576054575-0.1981972662040.1882579690470.463310376842-0.0240576007328-0.122572648006-0.131247559668-0.553973347171-0.481613269270.1941921529320.4736135906120.19313115475-0.1325735898330.587780693812-0.3041261366620.603692283911-21.353558430719.419374839916.7154967226
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 -2 through 10 )-2 - 101 - 13
22chain 'A' and (resid 11 through 31 )11 - 3114 - 34
33chain 'A' and (resid 32 through 83 )32 - 8335 - 67
44chain 'A' and (resid 84 through 126 )84 - 12668 - 110
55chain 'A' and (resid 127 through 138 )127 - 138111 - 122
66chain 'A' and (resid 139 through 164 )139 - 164123 - 148
77chain 'A' and (resid 165 through 195 )165 - 195149 - 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