[English] 日本語
Yorodumi
- PDB-3kwi: X-ray structure of NS1 effector domain W187Y mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kwi
TitleX-ray structure of NS1 effector domain W187Y mutant
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / influenza / NS1 / effector domain / Alternative splicing / Host cytoplasm / Host nucleus / Host-virus interaction / Interferon antiviral system evasion / RNA-binding / Suppressor of RNA silencing
Function / homology
Function and homology information


symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response ...symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / identical protein binding
Similarity search - Function
Influenza virus non-structural protein, effector domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsXia, S. / Robertus, J.D.
CitationJournal: Arch.Biochem.Biophys. / Year: 2010
Title: X-ray structures of NS1 effector domain mutants.
Authors: Xia, S. / Robertus, J.D.
History
DepositionDec 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)32,0292
Polymers32,0292
Non-polymers00
Water1,49583
1
A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)16,0141
Polymers16,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)16,0141
Polymers16,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.991, 60.236, 132.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 16014.423 Da / Num. of mol.: 2 / Fragment: NS1 effector domain / Mutation: W187Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: influenza A/Udorn/72 virus / Gene: NS / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P03495
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5
Details: 0.3M magnesium formate and 0.1M Bis-Tris , pH 5.5, EVAPORATION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 22, 2009 / Details: VARIMAX
RadiationMonochromator: VARIMAX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. all: 19795 / Num. obs: 18310 / % possible obs: 99 % / Redundancy: 10 % / Rmerge(I) obs: 0.048 / Rsym value: 0.041 / Net I/σ(I): 51.4
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 62.2 / Num. unique all: 1771 / Rsym value: 0.242 / % possible all: 90.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EE9

3ee9


Resolution: 2.21→36.12 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.059 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25762 983 5.1 %RANDOM
Rwork0.22184 ---
all0.22362 19795 --
obs0.22362 18310 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.428 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--0.93 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.21→36.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 0 83 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221923
X-RAY DIFFRACTIONr_bond_other_d00.021828
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.9762603
X-RAY DIFFRACTIONr_angle_other_deg0.51634243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29224.26882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74215353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0071513
X-RAY DIFFRACTIONr_chiral_restr0.0580.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212092
X-RAY DIFFRACTIONr_gen_planes_other00.02373
X-RAY DIFFRACTIONr_mcbond_it1.2331190
X-RAY DIFFRACTIONr_mcbond_other0.2213486
X-RAY DIFFRACTIONr_mcangle_it2.3451935
X-RAY DIFFRACTIONr_scbond_it3.5397733
X-RAY DIFFRACTIONr_scangle_it5.85111668
LS refinement shellResolution: 2.213→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 54 -
Rwork0.292 1155 -
obs--83.26 %

+
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