[English] 日本語
Yorodumi
- PDB-2ckn: NMR Structure of the First Ig Module of mouse FGFR1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ckn
TitleNMR Structure of the First Ig Module of mouse FGFR1
ComponentsBASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1
KeywordsTRANSFERASE / KINASE / HEPARIN-BINDING / NUCLEOTIDE-BINDING / IMMUNOGLOBULIN DOMAIN / ALTERNATICE SPLICING / ATP-BINDING / GLYCOPROTEIN / RECEPTOR / TYROSINE-PROTEIN KINASE
Function / homology
Function and homology information


postnatal olfactory bulb interneuron migration / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / FGFR1c and Klotho ligand binding and activation / Phospholipase C-mediated cascade: FGFR1 / regulation of phosphorus metabolic process / paraxial mesoderm development ...postnatal olfactory bulb interneuron migration / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / FGFR1c and Klotho ligand binding and activation / Phospholipase C-mediated cascade: FGFR1 / regulation of phosphorus metabolic process / paraxial mesoderm development / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / SHC-mediated cascade:FGFR1 / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / Signal transduction by L1 / regulation of phosphate transport / vitamin D3 metabolic process / PI3K Cascade / ear development / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Negative regulation of FGFR1 signaling / regulation of stem cell proliferation / middle ear morphogenesis / vasculogenesis involved in coronary vascular morphogenesis / orbitofrontal cortex development / diphosphate metabolic process / tangential migration from the subventricular zone to the olfactory bulb / branching involved in salivary gland morphogenesis / positive regulation of parathyroid hormone secretion / positive regulation of hepatic stellate cell activation / lung-associated mesenchyme development / auditory receptor cell development / organ induction / PIP3 activates AKT signaling / cementum mineralization / RAF/MAP kinase cascade / response to sodium phosphate / mesenchymal cell differentiation / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / receptor-receptor interaction / positive regulation of mesenchymal cell proliferation / regulation of postsynaptic density assembly / cell projection assembly / embryonic limb morphogenesis / fibroblast growth factor receptor activity / blood vessel morphogenesis / ureteric bud development / outer ear morphogenesis / inner ear morphogenesis / positive regulation of fibroblast migration / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / stem cell population maintenance / midbrain development / salivary gland morphogenesis / fibroblast growth factor receptor signaling pathway / generation of neurons / central nervous system neuron development / positive regulation of MAP kinase activity / chondrocyte differentiation / fibroblast growth factor binding / lung development / epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / negative regulation of osteoblast differentiation / positive regulation of cardiac muscle cell proliferation / cell maturation / calcium ion homeostasis / positive regulation of neuron differentiation / cellular response to fibroblast growth factor stimulus / positive regulation of cell cycle / peptidyl-tyrosine phosphorylation / sensory perception of sound / cell adhesion molecule binding / SH2 domain binding / brain development / positive regulation of cell differentiation / positive regulation of neuron projection development / in utero embryonic development / receptor protein-tyrosine kinase / gene expression / neuron projection development / regulation of gene expression / regulation of cell population proliferation / protein autophosphorylation / heparin binding / angiogenesis / protein tyrosine kinase activity / cytoplasmic vesicle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / signaling receptor complex / postsynapse / negative regulation of gene expression / signaling receptor binding / positive regulation of cell population proliferation
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain ...Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR
AuthorsKiselyov, V.V. / Bock, E. / Berezin, V. / Poulsen, F.M.
CitationJournal: Protein Sci. / Year: 2006
Title: NMR Structure of the First Ig Module of Mouse Fgfr1.
Authors: Kiselyov, V.V. / Bock, E. / Berezin, V. / Poulsen, F.M.
History
DepositionApr 20, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2Jan 15, 2020Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_cs
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)10,4621
Polymers10,4621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

-
Components

#1: Protein BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1 / FGFR-1 / BFGF-R / MFR


Mass: 10461.557 Da / Num. of mol.: 1 / Fragment: IG1 MODULE OF MOUSE FGFR1, RESIDUES 25-119 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse)
References: UniProt: P16092, receptor protein-tyrosine kinase
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

-
Sample preparation

Sample conditionsTemperature: 298.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002

-
Processing

NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 20

+
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