[English] 日本語
Yorodumi
- PDB-4hwu: Crystal structure of the Ig-C2 type 1 domain from mouse Fibroblas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hwu
TitleCrystal structure of the Ig-C2 type 1 domain from mouse Fibroblast growth factor receptor 2 (FGFR2) [NYSGRC-005912]
ComponentsFibroblast growth factor receptor 2
KeywordsIMMUNE SYSTEM / FGFR2 / KGFR / CD332 / Ig-C2 type 1 domain / Ig superfamily / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


coronal suture morphogenesis / FGFR2c ligand binding and activation / FGFR2b ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / urothelial cell proliferation / positive regulation of urothelial cell proliferation / endodermal digestive tract morphogenesis / SHC-mediated cascade:FGFR2 / PI-3K cascade:FGFR2 / mitotic nuclear division ...coronal suture morphogenesis / FGFR2c ligand binding and activation / FGFR2b ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / urothelial cell proliferation / positive regulation of urothelial cell proliferation / endodermal digestive tract morphogenesis / SHC-mediated cascade:FGFR2 / PI-3K cascade:FGFR2 / mitotic nuclear division / FRS-mediated FGFR2 signaling / fibroblast growth factor receptor apoptotic signaling pathway / PI3K Cascade / Negative regulation of FGFR2 signaling / lens fiber cell development / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / lateral sprouting from an epithelium / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / prostate gland morphogenesis / otic vesicle formation / regulation of smooth muscle cell differentiation / vasculogenesis involved in coronary vascular morphogenesis / regulation of morphogenesis of a branching structure / orbitofrontal cortex development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / morphogenesis of embryonic epithelium / RAF/MAP kinase cascade / bud elongation involved in lung branching / epidermis morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / PIP3 activates AKT signaling / reproductive structure development / limb bud formation / membranous septum morphogenesis / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / mesenchymal cell differentiation / epithelial cell proliferation involved in salivary gland morphogenesis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / branching involved in labyrinthine layer morphogenesis / mesenchymal cell proliferation involved in lung development / pyramidal neuron development / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation / regulation of osteoblast proliferation / branching involved in salivary gland morphogenesis / embryonic pattern specification / lung-associated mesenchyme development / outflow tract septum morphogenesis / regulation of epithelial cell proliferation / regulation of smoothened signaling pathway / negative regulation of mitotic nuclear division / bone morphogenesis / digestive tract development / odontogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / cardiac muscle cell proliferation / inner ear morphogenesis / organ growth / hair follicle morphogenesis / neuromuscular junction development / ventricular cardiac muscle tissue morphogenesis / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / synaptic vesicle transport / lung alveolus development / epithelial tube branching involved in lung morphogenesis / prostate epithelial cord elongation / midbrain development / positive regulation of stem cell proliferation / bone mineralization / fibroblast growth factor binding / positive regulation of cell division / excitatory synapse / positive regulation of Wnt signaling pathway / cell fate commitment / fibroblast growth factor receptor signaling pathway / canonical Wnt signaling pathway / embryonic organ development / regulation of ERK1 and ERK2 cascade / positive regulation of cardiac muscle cell proliferation / positive regulation of cell cycle / epithelial cell differentiation / ERK1 and ERK2 cascade / axonogenesis / positive regulation of epithelial cell proliferation / epithelial cell proliferation / post-embryonic development / animal organ morphogenesis
Similarity search - Function
Fibroblast growth factor receptor family / 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. ...Fibroblast growth factor receptor family / 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. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.903 Å
AuthorsKumar, P.R. / Ahmed, M. / Banu, R. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. ...Kumar, P.R. / Ahmed, M. / Banu, R. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Love, J. / Patel, H. / Rubinstein, R. / Seidel, R. / Stead, M. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of the Ig-C2 type 1 domain from mouse FGFR2 [NYSGRC-005912]
Authors: Kumar, P.R. / Nathenson, S.G. / Almo, S.C.
History
DepositionNov 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibroblast growth factor receptor 2
B: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)20,7572
Polymers20,7572
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-10 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.818, 53.818, 122.817
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer

-
Components

#1: Protein Fibroblast growth factor receptor 2 / FGFR-2 / Keratinocyte growth factor receptor / KGFR


Mass: 10378.567 Da / Num. of mol.: 2 / Fragment: UNP residues 45-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bek, Ect1, Fgfr2 / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5
References: UniProt: P21803, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (1.1M Malonic acid, 0.15M Ammonium Citrate Tribasic, 0.072M Succinic acid, 0.18M DL-Malic Acid, 0.24M Sodium acetate, 0.3M ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (1.1M Malonic acid, 0.15M Ammonium Citrate Tribasic, 0.072M Succinic acid, 0.18M DL-Malic Acid, 0.24M Sodium acetate, 0.3M Sodium formate, 0.096M Ammonium tartrate dibasic, pH 7.0), Cryoprotection (Reservoir + 20% Glycerol, a speck of I3C (Jena Biosciences) heavy atom), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.5498 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 8822 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.178 / Χ2: 1.3 / Net I/σ(I): 17.75
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.9-2.959.14300.9161100
2.95-310.14550.9221100
3-3.0611.14160.951100
3.06-3.1211.34540.91611000.875
3.12-3.1911.24550.98511000.719
3.19-3.2711.44171.01311000.544
3.27-3.3511.54641.05211000.586
3.35-3.4411.44231.14111000.449
3.44-3.5411.44471.18911000.387
3.54-3.65114301.74511000.469
3.65-3.7810.54332.24811000.28
3.78-3.9411.34521.79311000.25
3.94-4.1111.54441.48411000.166
4.11-4.3311.54301.39211000.137
4.33-4.611.54521.49211000.125
4.6-4.9611.54471.4711000.111
4.96-5.4611.44391.38311000.117
5.46-6.2411.34361.24511000.102
6.24-7.8611.24501.19711000.082
7.86-5011.34481.42111000.057

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.903→46.608 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7795 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 225 4.66 %RANDOM
Rwork0.2265 ---
obs0.2277 4833 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.6 Å2 / Biso mean: 22.2141 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.903→46.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 0 16 1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111192
X-RAY DIFFRACTIONf_angle_d1.4051621
X-RAY DIFFRACTIONf_chiral_restr0.076192
X-RAY DIFFRACTIONf_plane_restr0.007203
X-RAY DIFFRACTIONf_dihedral_angle_d14.4419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9031-3.65740.25311150.22152251236699
3.6574-46.61370.25171100.22862357246798

+
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