[English] 日本語
Yorodumi
- PDB-4oro: Structure of Influenza B PB2 cap-binding domain complex with GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oro
TitleStructure of Influenza B PB2 cap-binding domain complex with GDP
ComponentsPolymerase PB2
KeywordsVIRAL PROTEIN / cap binding
Function / homologyInfluenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA polymerase PB2 CAP binding domain / viral RNA genome replication / RNA binding / GUANOSINE-5'-DIPHOSPHATE / Polymerase PB2
Function and homology information
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, Y. / Zheng, X.
CitationJournal: to be published
Title: Structure of Influenza B PB2 cap-binding domain complex with GDP
Authors: Liu, Y. / Zheng, X.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase PB2
B: Polymerase PB2
C: Polymerase PB2
D: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2158
Polymers78,4424
Non-polymers1,7734
Water4,017223
1
A: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0542
Polymers19,6111
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0542
Polymers19,6111
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0542
Polymers19,6111
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0542
Polymers19,6111
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.420, 42.771, 118.414
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number3
Space group name H-MP121

-
Components

#1: Protein
Polymerase PB2 / Polymerase basic protein 2


Mass: 19610.619 Da / Num. of mol.: 4 / Fragment: cap-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Jiangxi/BV/2006 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KKU8*PLUS
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS FROM INFLUENZA B VIRUS (B/JIANGXI/BV/2006) WHICH WAS NOT SUBMITTED IN UNP. ...THIS SEQUENCE IS FROM INFLUENZA B VIRUS (B/JIANGXI/BV/2006) WHICH WAS NOT SUBMITTED IN UNP. RESIUDES 316-319 ARE THE EXPRESSION TAG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 20% PEG 3350, 0.2M potassium sodium tartrate, 0.1M Bis-Tris, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2014
RadiationMonochromator: Crystallogic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 33156 / Num. obs: 32029 / % possible obs: 96.6 % / Observed criterion σ(I): 3.5 / Redundancy: 4.3 %
Reflection shellResolution: 2.4→2.44 Å / % possible all: 96.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OR4

4or4


Resolution: 2.4→39.47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.339 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26982 1625 5.1 %RANDOM
Rwork0.19906 ---
obs0.20271 30304 95.88 %-
all-31606 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.745 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 112 223 5819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225684
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.9867600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7055672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33523.662284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.317151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6521556
X-RAY DIFFRACTIONr_chiral_restr0.1250.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024192
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9471.53320
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84325309
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.12832364
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1274.52291
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: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 104 -
Rwork0.211 2060 -
obs--89.53 %

+
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