[English] 日本語
Yorodumi
- PDB-6nrl: X-ray structure of H6N6-NS1 delta(80-84) R38A K41A E71G mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nrl
TitleX-ray structure of H6N6-NS1 delta(80-84) R38A K41A E71G mutant
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / Protein
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 / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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) / S15/NS1, RNA-binding / Helix Hairpins / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich ...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) / S15/NS1, RNA-binding / Helix Hairpins / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMitra, S. / Kumar, D. / Hu, L. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationQ1279 United States
CitationJournal: J.Virol. / Year: 2019
Title: Influenza A Virus Protein NS1 Exhibits Strain-Independent Conformational Plasticity.
Authors: Mitra, S. / Kumar, D. / Hu, L. / Sankaran, B. / Moosa, M.M. / Rice, A.P. / Ferreon, J.C. / Ferreon, A.C.M. / Prasad, B.V.V.
History
DepositionJan 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 11, 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: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)21,9991
Polymers21,9991
Non-polymers00
Water1267
1
A: Non-structural protein 1

A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)43,9982
Polymers43,9982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area1590 Å2
ΔGint-4 kcal/mol
Surface area23430 Å2
MethodPISA
2
A: Non-structural protein 1

A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)43,9982
Polymers43,9982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area1880 Å2
ΔGint-7 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.190, 105.190, 80.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Non-structural protein 1 / NS1


Mass: 21999.168 Da / Num. of mol.: 1 / Mutation: delta80-84, E71G, R38A, K41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2Y234
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium citrate, 0.1 M Tris hydrochloride pH 8.5, and 30% (v/v) PEG 400

-
Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999949 Å / Relative weight: 1
ReflectionResolution: 3.2→34.432 Å / Num. obs: 4652 / % possible obs: 99.61 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 2.1
Reflection shellResolution: 3.2→3.315 Å / Rmerge(I) obs: 0.163 / Num. unique obs: 661 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OPH

4oph


Resolution: 3.2→34.432 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 241 5.19 %
Rwork0.243 --
obs0.2442 4641 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→34.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 0 7 1532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041549
X-RAY DIFFRACTIONf_angle_d0.9012092
X-RAY DIFFRACTIONf_dihedral_angle_d6.492939
X-RAY DIFFRACTIONf_chiral_restr0.048238
X-RAY DIFFRACTIONf_plane_restr0.005272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2005-4.03130.32891170.27462131X-RAY DIFFRACTION100
4.0313-34.43350.23741240.23252269X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.3361 Å / Origin y: -40.2848 Å / Origin z: -1.461 Å
111213212223313233
T0.8108 Å20.0623 Å2-0.0975 Å2-0.899 Å2-0.0051 Å2--1.0079 Å2
L1.8962 °21.426 °2-1.7928 °2-1.4612 °2-2.1673 °2--5.1182 °2
S0.2962 Å °-0.1971 Å °0.2544 Å °0.3761 Å °0.0716 Å °0.5128 Å °-1.2938 Å °0.4253 Å °-0.0014 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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