[English] 日本語
Yorodumi
- PDB-4wsb: Bat Influenza A polymerase with bound vRNA promoter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wsb
TitleBat Influenza A polymerase with bound vRNA promoter
Components
  • (Influenza A polymerase vRNA promoter ...) x 2
  • Polymerase PA
  • Polymerase PB2
  • RNA-directed RNA polymerase catalytic subunit
Keywordstransferase/rna / transferase-rna complex
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / GTP binding / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : ...Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCusack, S. / Pflug, A. / Guilligay, D. / Reich, S.
CitationJournal: Nature / Year: 2014
Title: Structural insight into cap-snatching and RNA synthesis by influenza polymerase.
Authors: Reich, S. / Guilligay, D. / Pflug, A. / Malet, H. / Berger, I. / Crepin, T. / Hart, D. / Lunardi, T. / Nanao, M. / Ruigrok, R.W. / Cusack, S.
History
DepositionOct 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity.formula_weight / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Jan 10, 2024Group: 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: Polymerase PA
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase PB2
R: Influenza A polymerase vRNA promoter 3' end
V: Influenza A polymerase vRNA promoter 5' end
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,85722
Polymers273,2725
Non-polymers1,58517
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44420 Å2
ΔGint-382 kcal/mol
Surface area90510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.190, 149.320, 88.620
Angle α, β, γ (deg.)90.00, 98.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein Polymerase PA


Mass: 85490.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal extension: his-tag C-terminal extension: linker and TEV site
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)
Gene: PA / Plasmid: pKL-PBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM92
#2: Protein RNA-directed RNA polymerase catalytic subunit


Mass: 87936.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal extension: linker C-terminal extension: linker and TEV site
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)
Gene: PB1 / Plasmid: pKL-PBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM91, RNA-directed RNA polymerase
#3: Protein Polymerase PB2


Mass: 89012.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal extension: linker C-terminal extension: Strep-tag and TEV site
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)
Gene: PB2 / Plasmid: pKL-PBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM90

-
Influenza A polymerase vRNA promoter ... , 2 types, 2 molecules RV

#4: RNA chain Influenza A polymerase vRNA promoter 3' end


Mass: 5584.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus
#5: RNA chain Influenza A polymerase vRNA promoter 5' end


Mass: 5248.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus

-
Non-polymers , 3 types, 50 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Bat influenza polymerase protein in 50 mM HEPES-NaOH, 500 mM NaCl, 5 % glycerol, 2 mM TCEP, pH = 7.5 was adjusted to a concentration of 10 mg per ml, mixed in a 1:1 ratio with vRNA, which ...Details: Bat influenza polymerase protein in 50 mM HEPES-NaOH, 500 mM NaCl, 5 % glycerol, 2 mM TCEP, pH = 7.5 was adjusted to a concentration of 10 mg per ml, mixed in a 1:1 ratio with vRNA, which was an equimolar mixture of nucleotides 1-16 from the 5 prime end and nucleotides 1-18 or 3-18 from the 3 prime end. Protein-RNA was mixed with mother liquor containing 0.7-1.5 M sodium-potassium phosphate at pH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 99462 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.9
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.439 / Mean I/σ(I) obs: 1.14 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSA

4wsa


Resolution: 2.65→19.996 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 4752 4.78 %
Rwork0.2154 --
obs0.2179 99387 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: 1 / Resolution: 2.65→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17471 600 81 33 18185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418550
X-RAY DIFFRACTIONf_angle_d0.73225165
X-RAY DIFFRACTIONf_dihedral_angle_d13.917125
X-RAY DIFFRACTIONf_chiral_restr0.0292791
X-RAY DIFFRACTIONf_plane_restr0.0033125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6502-2.68020.41991550.40582865X-RAY DIFFRACTION91
2.6802-2.71170.41251540.37453148X-RAY DIFFRACTION100
2.7117-2.74460.38981830.3543144X-RAY DIFFRACTION100
2.7446-2.77930.40521620.34373141X-RAY DIFFRACTION100
2.7793-2.81580.37571300.33943184X-RAY DIFFRACTION100
2.8158-2.85420.38021630.34193186X-RAY DIFFRACTION100
2.8542-2.89490.39261670.32883126X-RAY DIFFRACTION100
2.8949-2.9380.35271430.30193167X-RAY DIFFRACTION100
2.938-2.98370.35841340.29463162X-RAY DIFFRACTION100
2.9837-3.03250.3731520.28653148X-RAY DIFFRACTION100
3.0325-3.08460.31651750.26453140X-RAY DIFFRACTION100
3.0846-3.14050.27841520.26963187X-RAY DIFFRACTION100
3.1405-3.20060.33021570.26143163X-RAY DIFFRACTION100
3.2006-3.26570.29711640.2493183X-RAY DIFFRACTION100
3.2657-3.33640.30921770.23413127X-RAY DIFFRACTION100
3.3364-3.41360.29091590.2323196X-RAY DIFFRACTION100
3.4136-3.49860.3061680.23183129X-RAY DIFFRACTION100
3.4986-3.59260.26391700.21863131X-RAY DIFFRACTION100
3.5926-3.69770.26721620.21953163X-RAY DIFFRACTION100
3.6977-3.81630.28021570.21123159X-RAY DIFFRACTION100
3.8163-3.95170.23561320.20933180X-RAY DIFFRACTION100
3.9517-4.10860.29191640.20543146X-RAY DIFFRACTION100
4.1086-4.29380.23381740.19463176X-RAY DIFFRACTION100
4.2938-4.51770.22861370.1933184X-RAY DIFFRACTION100
4.5177-4.79710.21431550.18733177X-RAY DIFFRACTION99
4.7971-5.16160.24561470.18593163X-RAY DIFFRACTION99
5.1616-5.67030.2511610.19963186X-RAY DIFFRACTION100
5.6703-6.46630.26051720.21553177X-RAY DIFFRACTION100
6.4663-8.05730.22651830.1993166X-RAY DIFFRACTION99
8.0573-19.99610.2351430.16533231X-RAY DIFFRACTION99

+
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