[English] 日本語
Yorodumi
- PDB-1n6v: Average structure of the interferon-binding ectodomain of the hum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n6v
TitleAverage structure of the interferon-binding ectodomain of the human type I interferon receptor
ComponentsInterferon-alpha/beta receptor beta chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / fibronectin fold / two-domain structure
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / JAK pathway signal transduction adaptor activity / response to interferon-beta / response to interferon-alpha / type I interferon-mediated signaling pathway / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling ...type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / JAK pathway signal transduction adaptor activity / response to interferon-beta / response to interferon-alpha / type I interferon-mediated signaling pathway / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / response to virus / cellular response to virus / Interferon alpha/beta signaling / defense response to virus / Potential therapeutics for SARS / cell surface receptor signaling pathway / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interferon alpha/beta receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model type detailsminimized average
AuthorsChill, J.H. / Quadt, S.R. / Levy, R. / Schreiber, G. / Anglister, J.
Citation
Journal: Structure / Year: 2003
Title: The human type I interferon receptor. NMR structure reveals the molecular basis of ligand binding.
Authors: Chill, J.H. / Quadt, S.R. / Levy, R. / Schreiber, G. / Anglister, J.
#1: Journal: Biochemistry / Year: 2002
Title: The human interferon receptor: NMR-based modeling, mapping of the IFN-alpha2 binding site, and observed ligand-induced tightening
Authors: Chill, J.H. / Nivasch, R. / Levy, R. / Albeck, S. / Schreiber, G. / Anglister, J.
History
DepositionNov 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interferon-alpha/beta receptor beta chain


Theoretical massNumber of molelcules
Total (without water)24,3231
Polymers24,3231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

-
Components

#1: Protein Interferon-alpha/beta receptor beta chain / IFNAR2-EC / IFN-alpha-REC / Type I interferon receptor / IFN-R / Interferon alpha/beta receptor- 2


Mass: 24323.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P48551

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
232HNCA
242HN(CA)CB
252CBCA(CO)NH
3633D 13C-separated NOESY
NMR detailsText: All experiments conducted in Shigemi tubes equipped with insert

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM U-15N IFNAR2-EC; 20mM d-Tris pH 8, 0.02% NaN395% H2O/5% D2O
20.35mM U-13C,15N IFNAR2-EC; 20mM d-Tris pH 8, 0.02% NaN395% H2O/5% D2O
30.3mM U-13C,15N IFNAR2-EC; 20mM d-Tris pH 8, 0.02% NaN399% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM Tris buffer 8 ambient 308 K
220mM Tris buffer 8 ambient 308 K
320mM Tris buffer 8 ambient 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX5002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Neidigprocessing
CNS1.1Brungerstructure solution
NMRPipe2.1Delagliodata analysis
CNS1.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: Structure based upon 1947 NOE-derived distance restraints (1066 of which long range), 172 dihedral angle restraints (of which 88 experimental and 84 TALOS-derived), 138 hydrogen-bond ...Details: Structure based upon 1947 NOE-derived distance restraints (1066 of which long range), 172 dihedral angle restraints (of which 88 experimental and 84 TALOS-derived), 138 hydrogen-bond restraints and 109 residual dipolar coupling restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

+
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