[English] 日本語
Yorodumi
- SASDGK2: Interleukin 11/Interleukin 11 receptor alpha complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDGK2
SampleInterleukin 11/Interleukin 11 receptor alpha complex
  • Interleukin-11 receptor subunit alpha (protein), IL11RA, Homo sapiens
  • Interleukin 11, N-terminal truncation (protein), IL11, Homo sapiens
Function / homology
Function and homology information


interleukin-11 receptor binding / interleukin-11 receptor activity / interleukin-11 binding / head development / interleukin-11-mediated signaling pathway / developmental process / IL-6-type cytokine receptor ligand interactions / cytokine activity / growth factor activity / cytokine-mediated signaling pathway ...interleukin-11 receptor binding / interleukin-11 receptor activity / interleukin-11 binding / head development / interleukin-11-mediated signaling pathway / developmental process / IL-6-type cytokine receptor ligand interactions / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / cell population proliferation / positive regulation of MAPK cascade / receptor complex / external side of plasma membrane / positive regulation of cell population proliferation / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Interleukin-11, mammalian / Interleukin-11 / Interleukin 11 / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Four-helical cytokine-like, core / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Interleukin-11, mammalian / Interleukin-11 / Interleukin 11 / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Four-helical cytokine-like, core / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin 11 / Interleukin-11 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Contact author
  • Riley D. Metcalfe (Bio21 Institute, The University of Melbourne, Melbourne, Australia)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3567
Type: atomic / Comment: Model generated using RosettaDock server. / Chi-square value: 1.074 / P-value: 0.734138
Model #3568
Type: dummy / Radius of dummy atoms: 2.75 A / Chi-square value: 1.035 / P-value: 0.963479

-
Sample

SampleName: Interleukin 11/Interleukin 11 receptor alpha complex / Specimen concentration: 2.2 mg/ml / Entity id: 1803 / 1804
BufferName: 20 mM Tris, 150 mM NaCl, 0.2% sodium azide / pH: 8.5
Entity #1803Name: IL11RA / Type: protein / Description: Interleukin-11 receptor subunit alpha / Formula weight: 32.179 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q14626
Sequence: GSSPCPQAWG PPGVQYGQPG RSVKLCCPGV TAGDPVSWFR DGEPKLLQGP DSGLGHELVL AQADSTDEGT YICQTLDGAL GGTVTLQLGY PPARPVVSCQ AADYENFSCT WSPSQISGLP TRYLTSYRKK TVLGADSQRR SPSTGPWPCP QDPLGAARCV VHGAEFWSQY ...Sequence:
GSSPCPQAWG PPGVQYGQPG RSVKLCCPGV TAGDPVSWFR DGEPKLLQGP DSGLGHELVL AQADSTDEGT YICQTLDGAL GGTVTLQLGY PPARPVVSCQ AADYENFSCT WSPSQISGLP TRYLTSYRKK TVLGADSQRR SPSTGPWPCP QDPLGAARCV VHGAEFWSQY RINVTEVNPL GASTRLLDVS LQSILRPDPP QGLRVESVPG YPRRLRASWT YPASWPSQPH FLLKFRLQYR PAQHPAWSTV EPAGLEEVIT DAVAGLPHAV RVSARDFLDA GTWSTWSPEA WGTPSTGT
Entity #1804Name: IL11 / Type: protein / Description: Interleukin 11, N-terminal truncation / Formula weight: 18.249 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: A8K3F7
Sequence:
GSPDPRAELD STVLLTRSLL ADTRQLAAQL RDKFPADGDH NLDSLPTLAM SAGALGALQL PGVLTRLRAD LLSYLRHVQW LRRAGGSSLK TLEPELGTLQ ARLDRLLRRL QLLMSRLALP QPPPDPPAPP LAPPSSAWGG IRAAHAILGG LHLTLDWAVR GLLLLKTRL

-
Experimental information

BeamInstrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / : Australia / Type of source: X-ray synchrotron / Wavelength: 0.1078 Å / Dist. spec. to detc.: 2.539 mm
DetectorName: Dectris/Pilatus3 S 2M / Pixsize x: 172 mm
Scan
Title: Interleukin 11/Interleukin 11 receptor alpha complex / Measurement date: Jun 8, 2019 / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 6 / Unit: 1/A /
MinMax
Q0.0059 0.5341
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 197 /
MinMax
Q0.00829081 0.163005
P(R) point1 197
R0 102
Result
Type of curve: sec /
ExperimentalPorod
MW50.1 kDa53 kDa
Volume-84 nm3

P(R)GuinierGuinier error
Forward scattering, I00.009356 0.009368 6.4E-5
Radius of gyration, Rg3.34 nm3.307 nm0.037

MinMax
D-10.2
Guinier point4 43

+
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