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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6whm
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease wild type bound to DNA oligomer TAGC (cleaved TTAGCATT, 5mM overnight DNA soak)
Components
  • DNA (5'-D(P*TP*AP*GP*C)-3')
  • PA-X protein,Polymerase acidic protein
KeywordsVIRAL PROTEIN/DNA / NUCLEASE / INFLUENZA / DNA oligomer / cleaved / VIRAL PROTEIN / VIRAL PROTEIN-DNA complex / DNA BINDING PROTEIN
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
: / DNA / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsCuypers, M.G. / Kumar, G. / Webb, T. / White, S.W.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Authors: Kumar, G. / Cuypers, M. / Webby, R.R. / Webb, T.R. / White, S.W.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PA-X protein,Polymerase acidic protein
B: DNA (5'-D(P*TP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0459
Polymers25,5652
Non-polymers4807
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-56 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.885, 89.885, 134.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
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 on special symmetry positions
IDModelComponents
11A-426-

HOH

-
Components

-
Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein PA-X 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))
Cell line: 2009/H1N1/CALIFORNIA / Gene: PA-X, PA / Variant: 2009/H1N1/CALIFORNIA / Strain: A/Luxembourg/43/2009(H1N1) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A481PFF5, UniProt: C6H0Y9
#2: DNA chain DNA (5'-D(P*TP*AP*GP*C)-3')


Mass: 2416.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

-
Non-polymers , 5 types, 143 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 0.02M MGCL2, 0.02M MNCL2.
Temp details: controlled Temperature room

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 21245 / % possible obs: 99.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 39.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Net I/σ(I): 46.4
Reflection shellResolution: 1.92→1.99 Å / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2 / Num. unique obs: 2048 / CC1/2: 0.786 / Rpim(I) all: 0.308 / Rrim(I) all: 0.74 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 1.92→37.35 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 983 4.63 %
Rwork0.1772 20252 -
obs0.179 21235 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.86 Å2 / Biso mean: 59.2088 Å2 / Biso min: 28.91 Å2
Refinement stepCycle: final / Resolution: 1.92→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 82 25 136 1673
Biso mean--109.99 64.67 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-2.020.29981310.25792791292298
2.02-2.150.22321290.206728873016100
2.15-2.320.25541320.18628582990100
2.32-2.550.21751560.185528523008100
2.55-2.920.20611580.187928803038100
2.92-3.680.25051200.179329493069100
3.68-37.350.19561570.16173035319299
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)
16.32711.66474.92642.2291.30377.90820.11330.7544-0.2214-0.1516-0.04540.01490.51650.4621-0.07980.4744-0.03210.17830.397-0.00690.3925125.0336200.9506276.5012
28.31430.23120.55222.9199-0.69572.27430.3279-0.03420.16910.1055-0.3205-0.08020.27320.13160.00450.4346-0.02120.1130.32560.09190.3271138.1961201.024290.5245
38.84245.10221.30334.4339-1.54766.460.5369-0.3625-1.0489-0.0088-0.398-0.26861.0655-0.0473-0.14510.6937-0.15380.12620.40710.09960.4943127.3521193.6817296.3051
45.0088-0.59683.14480.80280.39036.94390.123-0.4052-0.130.0284-0.16080.10590.5613-0.72960.01410.4162-0.13510.18480.3374-0.00420.3979117.5274203.6061289.7197
50.5660.28470.59074.7036-5.40987.7573-0.9354-0.5079-3.4639-2.8905-0.1671-2.17912.74360.51161.34111.7786-0.32180.80311.0780.40442.1463122.4721189.5782285.6444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 51 )A-2 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 107 )A52 - 107
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 130 )A108 - 130
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 175 )A131 - 175
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 4 )B1 - 4

+
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