[English] 日本語
Yorodumi
- PDB-6sw8: Crystal structure of the NS1 (H7N1) RNA-binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sw8
TitleCrystal structure of the NS1 (H7N1) RNA-binding domain
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / INFLUENZA VIRUS / RNA-BINDING DOMAIN / RNA BINDING PROTEIN
Function / homology
Function and homology information


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 / 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 A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.933 Å
AuthorsCoste, F. / Wacquiez, A. / Marc, D. / Castaing, B.
CitationJournal: Viruses / Year: 2020
Title: Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1.
Authors: Wacquiez, A. / Coste, F. / Kut, E. / Gaudon, V. / Trapp, S. / Castaing, B. / Marc, D.
History
DepositionSep 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,0337
Polymers17,6342
Non-polymers3985
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint1 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.827, 83.827, 68.527
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Non-structural protein 1 / NS1


Mass: 8817.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/turkey/Italy/977/1999(H7N1))
Strain: A/turkey/Italy/977/1999(H7N1) / Gene: ns1, NS, NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1PST0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12M (Diethylene glycol, Triethylene glycol, Tetraethylene glycol, Pentaethylene glycol) + 0.1M (Sodium HEPES, MOPS) + 37.5% (MPD, PEG 1000, PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98009 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 1.93→49.832 Å / Num. obs: 21170 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 42.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.9
Reflection shellResolution: 1.93→1.97 Å / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 21170 / CC1/2: 0.704

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H5N

5h5n


Resolution: 1.933→49.832 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.28
RfactorNum. reflection% reflection
Rfree0.1932 977 4.62 %
Rwork0.1755 --
obs0.1763 21170 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.85 Å2 / Biso mean: 54.5362 Å2 / Biso min: 29.11 Å2
Refinement stepCycle: final / Resolution: 1.933→49.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 26 66 1255
Biso mean--75.5 51.16 -
Num. residues----146
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)
16.09281.61370.59248.0147-2.90486.91280.00430.31540.3422-0.35480.35921.23110.0953-0.4929-0.34810.2737-0.0831-0.03630.35240.01190.399624.9599-23.9772-1.011
24.75963.7501-2.83865.7415-5.16676.8228-0.93760.9225-0.0494-1.91490.609-0.51030.4653-0.58720.27040.5766-0.184-0.05760.59860.0030.408927.4299-26.8016-9.2266
34.9642.0251.6335.18420.18694.45590.334-0.90830.48650.9415-0.45780.965-0.0749-0.86220.24320.5134-0.10270.11370.4672-0.00240.498323.1313-27.33288.2572
43.8481.75940.13564.7304-2.88966.88920.26430.03610.36130.2632-0.09250.4619-0.49960.1156-0.31750.3202-0.05420.06960.2932-0.02960.365332.7822-15.8682.129
52.01272.1438-0.86954.736-2.18613.4210.1634-0.0890.33980.36410.07380.2864-0.4216-0.0665-0.13770.3839-0.02690.04340.318-0.01040.326633.5801-16.35561.8359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 29 )B1 - 29
2X-RAY DIFFRACTION2chain 'B' and (resid 30 through 50 )B30 - 50
3X-RAY DIFFRACTION3chain 'B' and (resid 51 through 73 )B51 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 25 )A1 - 25
5X-RAY DIFFRACTION5chain 'A' and (resid 26 through 73 )A26 - 73

+
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