[English] 日本語
Yorodumi
- PDB-3l56: Crystal structure of the large c-terminal domain of polymerase ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l56
TitleCrystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/viet nam/1203/2004 (h5n1)
ComponentsPolymerase PB2
KeywordsVIRAL PROTEIN / Bird Flu / H5N1 / PB2 / polymerase / Host mitochondrion / mRNA capping / mRNA processing / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Polymerase Basic Protein 2, C-terminal domain / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain ...Polymerase Basic Protein 2, C-terminal domain / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / 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 helical domain / Influenza RNA polymerase PB2 CAP binding domain / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStaker, B.L. / Edwards, T. / Eric, S. / Raymond, A. / Stewart, L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos Pathog. / Year: 2010
Title: Biological and structural characterization of a host-adapting amino acid in influenza virus.
Authors: Yamada, S. / Hatta, M. / Staker, B.L. / Watanabe, S. / Imai, M. / Shinya, K. / Sakai-Tagawa, Y. / Ito, M. / Ozawa, M. / Watanabe, T. / Sakabe, S. / Li, C. / Kim, J.H. / Myler, P.J. / Phan, I. ...Authors: Yamada, S. / Hatta, M. / Staker, B.L. / Watanabe, S. / Imai, M. / Shinya, K. / Sakai-Tagawa, Y. / Ito, M. / Ozawa, M. / Watanabe, T. / Sakabe, S. / Li, C. / Kim, J.H. / Myler, P.J. / Phan, I. / Raymond, A. / Smith, E. / Stacy, R. / Nidom, C.A. / Lank, S.M. / Wiseman, R.W. / Bimber, B.N. / O'Connor, D.H. / Neumann, G. / Stewart, L.J. / Kawaoka, Y.
History
DepositionDec 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3May 23, 2012Group: Database references
Revision 1.4Sep 6, 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: Polymerase PB2
B: Polymerase PB2


Theoretical massNumber of molelcules
Total (without water)49,5392
Polymers49,5392
Non-polymers00
Water2,846158
1
A: Polymerase PB2


Theoretical massNumber of molelcules
Total (without water)24,7701
Polymers24,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase PB2


Theoretical massNumber of molelcules
Total (without water)24,7701
Polymers24,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.042, 57.007, 83.081
Angle α, β, γ (deg.)90.00, 102.40, 90.00
Int Tables number4
Space group name H-MP1211
DetailsUNKNOWN

-
Components

#1: Protein Polymerase PB2 / Polymerase basic subunit 2 / Polymerase protein PB2


Mass: 24769.527 Da / Num. of mol.: 2 / Fragment: Large C-terminal Domain, residues 538-759
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/VIET NAM/1203/2004 (H5N1) / Gene: PB2 / Plasmid: PET28-SMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNN3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.92 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 200MM NACL, 100MM TRIS PH 8.5, PROTEIN CONCENTRATION 24.4 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: SATURN 944++ / Detector: CCD / Date: Nov 9, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→81.14 Å / Num. obs: 16536 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 54
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.046 / % possible all: 82

-
Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0104refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KC6

3kc6


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.886 / SU B: 6.672 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.465 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.237 840 5.1 %RANDOM
Rwork0.176 ---
obs0.18 16526 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.46 Å2
2---0.26 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 0 158 3258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223170
X-RAY DIFFRACTIONr_bond_other_d0.0010.022198
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.974289
X-RAY DIFFRACTIONr_angle_other_deg0.89235359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47423.881134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81515564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2681524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
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_it0.731.51987
X-RAY DIFFRACTIONr_mcbond_other0.1381.5813
X-RAY DIFFRACTIONr_mcangle_it1.37323204
X-RAY DIFFRACTIONr_scbond_it1.96631183
X-RAY DIFFRACTIONr_scangle_it3.1424.51084
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 53 -
Rwork0.198 940 -
obs--81.19 %

+
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