[English] 日本語
Yorodumi
- PDB-3m5r: Crystal Structure of Swine Flu Virus NS1 Effector Domain from H1N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m5r
TitleCrystal Structure of Swine Flu Virus NS1 Effector Domain from H1N1 Influenza A/California/07/2009
ComponentsNonstructural protein 1
KeywordsVIRAL PROTEIN / Swine Flu Virus / Influenza A H1N1 Subtype / Nonstructural Protein 1 / Effector domain / Viral immune evasion / Structural Genomics / NIAID / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / host cell nucleus / RNA 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 / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsFremont, D.H. / Yu, Y.Y.L. / Nelson, C.A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Swine Flu Virus NS1 Effector Domain from H1N1 Influenza A/California/07/2009
Authors: Fremont, D.H. / Yu, Y.Y.L. / Nelson, C.A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nonstructural protein 1
B: Nonstructural protein 1
D: Nonstructural protein 1
E: Nonstructural protein 1
F: Nonstructural protein 1
G: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)90,2306
Polymers90,2306
Non-polymers00
Water5,188288
1
A: Nonstructural protein 1
B: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)30,0772
Polymers30,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-13 kcal/mol
Surface area12200 Å2
2
D: Nonstructural protein 1
E: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)30,0772
Polymers30,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Nonstructural protein 1
G: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)30,0772
Polymers30,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.530, 70.795, 96.685
Angle α, β, γ (deg.)90.000, 110.300, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Nonstructural protein 1


Mass: 15038.358 Da / Num. of mol.: 6 / Fragment: C-TERMINAL EFFECTOR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/07/2009 (H1N1) / Gene: NS1 / Plasmid: pET28A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: D2Y6Z6, UniProt: C3W611*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.7 M NaCl, 10% Ethanol and 0.1 M hexamine cobalt (III) chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 61983 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.061 / Χ2: 1.009 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.073.80.49661701.051100
2.07-2.153.80.38861420.951100
2.15-2.253.80.32761551.02299.9
2.25-2.373.80.20761911.018100
2.37-2.523.80.15661860.987100
2.52-2.713.80.11961691.011100
2.71-2.993.80.08862100.99100
2.99-3.423.80.06861771100
3.42-4.313.80.04462501.02999.9
4.31-1003.70.03663331.0399.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F5T

3f5t


Resolution: 2→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.803 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1550 2.7 %RANDOM
Rwork0.207 ---
obs0.208 57329 91.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.955 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 91.98 Å2 / Biso mean: 40.529 Å2 / Biso min: 18.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.217 Å20 Å24.255 Å2
2--5.504 Å20 Å2
3----5.287 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 0 288 6136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085964
X-RAY DIFFRACTIONf_angle_d1.1048086
X-RAY DIFFRACTIONf_chiral_restr0.069932
X-RAY DIFFRACTIONf_plane_restr0.0041026
X-RAY DIFFRACTIONf_dihedral_angle_d14.72216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0790.3091270.2584659478677
2.079-2.1620.321430.2455121526485
2.162-2.260.3431370.2585206534386
2.26-2.380.2621520.2285302545488
2.38-2.5290.2691520.2255640579293
2.529-2.7240.2741670.2315759592695
2.724-2.9980.2621600.2285877603797
2.998-3.4320.2441740.2065992616699
3.432-4.3230.21660.1756052621899
4.323-500.2141720.196171634399

+
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