[English] 日本語
Yorodumi
- PDB-4p9a: X-ray Crystal Structure of PA protein from Influenza strain H7N9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p9a
TitleX-ray Crystal Structure of PA protein from Influenza strain H7N9
ComponentsPolymerase PA
KeywordsVIRAL PROTEIN / PA protein Influenza H7N9 polymerase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / viral translational frameshifting / viral RNA genome replication / 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
Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1999 Å
AuthorsFairman, J.W. / Moen, S.O. / Clifton, M.C. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Rep / Year: 2014
Title: Structural analysis of H1N1 and H7N9 influenza A virus PA in the absence of PB1.
Authors: Moen, S.O. / Abendroth, J. / Fairman, J.W. / Baydo, R.O. / Bullen, J. / Kirkwood, J.L. / Barnes, S.R. / Raymond, A.C. / Begley, D.W. / Henkel, G. / McCormack, K. / Tam, V.C. / Phan, I. / ...Authors: Moen, S.O. / Abendroth, J. / Fairman, J.W. / Baydo, R.O. / Bullen, J. / Kirkwood, J.L. / Barnes, S.R. / Raymond, A.C. / Begley, D.W. / Henkel, G. / McCormack, K. / Tam, V.C. / Phan, I. / Staker, B.L. / Stacy, R. / Myler, P.J. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4302
Polymers53,3381
Non-polymers921
Water1,65792
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-1 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.890, 68.890, 400.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Polymerase PA


Mass: 53338.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/chicken/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: M9V5W3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 400 nl of protein solution at 20.77 mg/ml plus 400 nl precipitant solution equilibrated against 80 uL of precipitant. Precipitant: Wizard 3/4 well A10 - 200 mM sodium thiocyanate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 20, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1999→50 Å / Num. obs: 30002 / Observed criterion σ(I): -3 / Redundancy: 5.87 % / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.063 / Χ2: 0.97 / Net I/σ(I): 19.93
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1999-2.260.810.5853.113101216121610.641100
2.26-2.320.880.4414.0112507208720870.484100
2.32-2.390.9130.3954.5812549207720770.433100
2.39-2.460.9410.3025.8911937199519940.33299.9
2.46-2.540.9740.2297.6611678193519350.251100
2.54-2.630.9750.2048.4811109186018600.224100
2.63-2.730.9830.16810.0910987182818280.184100
2.73-2.840.9910.1312.4610498175517550.143100
2.84-2.970.9940.09716.539999167916790.106100
2.97-3.110.9960.07720.149703163016300.084100
3.11-3.280.9970.06323.839201155815580.07100
3.28-3.480.9980.0529.68569146014590.05599.9
3.48-3.720.9980.0436.778112139313930.044100
3.72-4.020.9990.03640.217547131813170.0499.9
4.02-4.40.9990.03145.236905120912050.03599.7
4.4-4.920.9990.0346.636239112311220.03399.9
4.92-5.680.9990.02945.6355539949940.032100
5.68-6.960.9990.02844.0846418718590.03298.6
6.96-9.840.9990.02451.1736057016900.02698.4
9.84-500.9990.02251.0217994403990.02590.7

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZNL

2znl


Resolution: 2.1999→35.653 Å / FOM work R set: 0.851 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1466 4.89 %Random
Rwork0.2027 28528 --
obs0.204 29994 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.67 Å2 / Biso mean: 58.06 Å2 / Biso min: 27.04 Å2
Refinement stepCycle: final / Resolution: 2.1999→35.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 6 92 3010
Biso mean--91.58 48.51 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083018
X-RAY DIFFRACTIONf_angle_d0.9754099
X-RAY DIFFRACTIONf_chiral_restr0.038467
X-RAY DIFFRACTIONf_plane_restr0.004520
X-RAY DIFFRACTIONf_dihedral_angle_d12.841091
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1999-2.27850.24711500.215227652915100
2.2785-2.36980.23891410.21327872928100
2.3698-2.47760.23931420.212327822924100
2.4776-2.60820.25171310.209527822913100
2.6082-2.77150.27151340.222528352969100
2.7715-2.98540.22861220.230128582980100
2.9854-3.28570.26991580.218628172975100
3.2857-3.76070.19881580.189228683026100
3.7607-4.73630.20661710.172729013072100
4.7363-35.65720.22981590.21023133329298
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)
11.93811.3999-1.55662.05110.19993.16870.1788-0.21970.2331-0.04-0.2392-0.1477-0.1923-0.0104-0.06760.18830.04350.03690.6180.07590.303618.757431.361214.2697
23.5630.6467-0.7131.83421.05563.69610.00030.38170.4355-0.0842-0.12140.2042-0.39590.07470.01130.2227-0.03760.02120.64610.1390.377526.17939.19570.3221
31.39670.09251.20831.7742-0.24433.2454-0.2467-0.0147-0.56420.4093-0.2022-0.18690.53940.77350.23930.28410.03560.01050.75140.14610.430223.990321.30319.6796
42.45230.283-0.20531.79280.08973.47340.0507-0.1782-0.09020.233-0.00810.182-0.1073-0.3345-0.03910.19460.05860.0290.58170.1150.328413.009630.61813.1837
51.72490.35690.70673.7841-1.87681.3816-0.09110.0176-0.48190.5539-0.30470.67340.5877-0.71110.20040.5592-0.18460.17160.7370.09070.5258.191614.405826.8262
62.03021.3767-0.84433.828-3.82694.3561-0.17070.0801-0.7616-0.2557-0.5391-0.68781.11020.05890.64770.6348-0.00540.18680.7230.20970.574719.2334.942326.9213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 313 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 314 through 369 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 370 through 415 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 416 through 596 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 597 through 671 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 672 through 713 )A0

+
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