[English] 日本語
Yorodumi
- PDB-5wop: High Resolution Structure of Mutant CA09-PB2cap -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wop
TitleHigh Resolution Structure of Mutant CA09-PB2cap
ComponentsPolymerase PB2
KeywordsTRANSCRIPTION / Polymerase Basic Protein 2 / Cap-Snatching / RNA Polymerase / Influenza / Cap-Binding Domain / Structural Genomics
Function / homologyInfluenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA polymerase PB2 CAP binding domain / host cell mitochondrion / viral RNA genome replication / RNA binding / Polymerase PB2
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsConstantinides, A.E. / Gumpper, R.H. / Severin, C. / Luo, M.
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: High-resolution structure of the Influenza A virus PB2cap binding domain illuminates the changes induced by ligand binding.
Authors: Constantinides, A. / Gumpper, R. / Severin, C. / Luo, M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: The cap-binding site of influenza virus protein PB2 as a drug target
Authors: Severin, C. / Rocha de Moura, T. / Liu, Y. / Li, K. / Zheng, X. / Luo, M.
#2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization and X-ray crystallographic analysis of the cap-binding domain of influenza A virus H1N1 polymerase subunit PB2
Authors: Liu, Y. / Meng, G. / Luo, M. / Zheng, X.
History
DepositionAug 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Revision 1.2Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0446
Polymers35,6752
Non-polymers3684
Water6,053336
1
A: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1144
Polymers17,8381
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9302
Polymers17,8381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.863, 72.429, 61.316
Angle α, β, γ (deg.)90.000, 103.180, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Polymerase PB2 / Mutant CA09-PB2cap


Mass: 17837.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PB2 / Production host: Escherichia coli (E. coli) / References: UniProt: F4MEU3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.24 Å3/Da / Density % sol: 45.21 % / Description: Prism
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.86
Details: 0.1 M ammonium acetate, 0.1 M Bis Tris, pH 5.86, 20% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2017
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→72.43 Å / Num. obs: 47950 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.042 / Rrim(I) all: 0.076 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.52-1.553.20.6310.8090.4250.763100
8.33-72.4330.0260.9990.0180.03194.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EG7

5eg7


Resolution: 1.52→39 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.059 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 2438 5.1 %RANDOM
Rwork0.1478 ---
obs0.1511 45487 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.43 Å2 / Biso mean: 21.183 Å2 / Biso min: 2.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.05 Å2
2---0.97 Å2-0 Å2
3---1.64 Å2
Refinement stepCycle: final / Resolution: 1.52→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 48 336 2873
Biso mean--86.39 31.54 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192543
X-RAY DIFFRACTIONr_bond_other_d0.0130.022475
X-RAY DIFFRACTIONr_angle_refined_deg2.2391.9663396
X-RAY DIFFRACTIONr_angle_other_deg1.19735721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25523.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.915493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3021524
X-RAY DIFFRACTIONr_chiral_restr0.1550.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022768
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02528
X-RAY DIFFRACTIONr_rigid_bond_restr4.13735015
X-RAY DIFFRACTIONr_sphericity_free26.6635219
X-RAY DIFFRACTIONr_sphericity_bonded13.34455102
LS refinement shellResolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 194 -
Rwork0.273 3369 -
all-3563 -
obs--99.97 %
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)
10.0576-0.01430.00790.190.00090.0012-0.00140.00460.00090.00130.0013-0.01120.0001-0.00040.00010.00530.00070.00610.01180.00040.015-6.37050.164628.4877
20.0463-0.04460.01230.2194-0.00880.0037-0.00130.0037-0.00160.00450.0031-0.00710.00020.0015-0.00180.00510.00040.00510.0128-0.00040.0150.57121.9374-1.4207
30.001-0.0033-0.00040.027-0.00130.00370.00060.0018-0.00130.0026-0.0030.00150.00060.00140.00240.00480.00030.00280.0128-0.00010.0224-5.24330.88616.742
41.9906-2.00732.38462.6286-2.06753.09610.17280.42260.10050.0172-0.2333-0.07990.20390.65870.06050.33750.0150.26520.19620.00410.3925-5.7071-2.593513.97
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A321 - 761
2X-RAY DIFFRACTION2B4 - 479
3X-RAY DIFFRACTION3C1 - 276
4X-RAY DIFFRACTION4D1 - 6

+
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