[English] 日本語
Yorodumi
- PDB-5fmz: Crystal structure of Influenza B polymerase with bound 5' vRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fmz
TitleCrystal structure of Influenza B polymerase with bound 5' vRNA
Components
  • 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'
  • POLYMERASE ACIDIC PROTEIN
  • POLYMERASE BASIC PROTEIN 2
  • RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
KeywordsTRANSCRIPTION / INFLUENZA B VIRUS RNA-DEPENDENT RNA POLYMERASE / HETEROTRIMER / VIRAL RNA / VRNA 5' END.
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / 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-dependent RNA polymerase subunit PB2 / 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 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / 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 / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA / RNA (> 10) / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesINFLUENZA B VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsGuilligay, D. / Cusack, S.
Citation
Journal: Mol.Cell / Year: 2016
Title: Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of Pb2 Domains.
Authors: Thierry, E. / Guilligay, D. / Kosinski, J. / Bock, T. / Gaudon, S. / Round, A. / Pflug, A. / Hengrung, N. / El Omari, K. / Baudin, F. / Hart, D.J. / Beck, M. / Cusack, S.
#1: Journal: Nature / Year: 2014
Title: Structure of Influenza a Polymerase Bound to the Viral RNA Promoter.
Authors: Pflug, A. / Guilligay, D. / Reich, S. / Cusack, S.
History
DepositionNov 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POLYMERASE ACIDIC PROTEIN
B: RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
C: POLYMERASE BASIC PROTEIN 2
D: POLYMERASE ACIDIC PROTEIN
E: RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
F: POLYMERASE BASIC PROTEIN 2
H: 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'
V: 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)533,5158
Polymers533,5158
Non-polymers00
Water00
1
D: POLYMERASE ACIDIC PROTEIN
E: RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
F: POLYMERASE BASIC PROTEIN 2
H: 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)266,7574
Polymers266,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38110 Å2
ΔGint-232.4 kcal/mol
Surface area87760 Å2
MethodPISA
2
A: POLYMERASE ACIDIC PROTEIN
B: RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
C: POLYMERASE BASIC PROTEIN 2
V: 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)266,7574
Polymers266,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37780 Å2
ΔGint-227 kcal/mol
Surface area87230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.570, 200.540, 133.130
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein POLYMERASE ACIDIC PROTEIN / INFLUENZA B POLYMERASE PA SUBUNIT


Mass: 85822.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA B VIRUS (B/MEMPHIS/13/2003) / Plasmid: PKL-PBAC / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q5V8Z9
#2: Protein RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT / INFLUENZA B POLYMERASE PB1 SUBUNIT


Mass: 86207.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA B VIRUS (B/MEMPHIS/13/2003) / Plasmid: PKL-PBAC / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase
#3: Protein POLYMERASE BASIC PROTEIN 2 / INFLUENZA B POLYMERASE PB2 SUBUNIT


Mass: 90844.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA B VIRUS (B/MEMPHIS/13/2003) / Plasmid: PKL-PBAC / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q5V8X3
#4: RNA chain 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3' / VRNA 5' END


Mass: 3883.408 Da / Num. of mol.: 2 / Fragment: FIRST 12 NUCLEOTIDES / Source method: obtained synthetically / Source: (synth.) INFLUENZA B VIRUS (B/MEMPHIS/13/2003)
Sequence detailsN-TERMINAL EXTENSION, HIS-TAG AND LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE N-TERMINAL ...N-TERMINAL EXTENSION, HIS-TAG AND LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE N-TERMINAL EXTENSION, LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE N-TERMINAL EXTENSION, LINKER. C-TERMINAL EXTENSION, LINKER, STREP-TAG AND TEV SITE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.7 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M KCL, 10 MM MGCL2, 50 MM TRIS-HCL PH 8.5 AND 30% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07228
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07228 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 86591 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.37 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 7.83
Reflection shellResolution: 3.4→3.55 Å / Redundancy: 6.11 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.66 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4WSA

4wsa


Resolution: 3.4→126.83 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.878 / SU B: 46.772 / SU ML: 0.674 / Cross valid method: THROUGHOUT / ESU R Free: 0.611 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27696 2595 3 %RANDOM
Rwork0.2553 ---
obs0.25595 83996 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.884 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å2-0.12 Å2
2---9.99 Å20 Å2
3---7.19 Å2
Refinement stepCycle: LAST / Resolution: 3.4→126.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34112 524 0 0 34636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01935345
X-RAY DIFFRACTIONr_bond_other_d0.0010.0233992
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.95547719
X-RAY DIFFRACTIONr_angle_other_deg0.853378433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68654265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48124.3581565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.104156570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.11615228
X-RAY DIFFRACTIONr_chiral_restr0.0530.25239
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02139123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027911
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6211.17617119
X-RAY DIFFRACTIONr_mcbond_other1.61911.17617118
X-RAY DIFFRACTIONr_mcangle_it2.9116.75721364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.15811.17818226
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 165 -
Rwork0.383 6197 -
obs--99.5 %

+
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://pdbjlvh1.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