[English] 日本語
Yorodumi
- PDB-2fdb: Crystal Structure of Fibroblast growth factor (FGF)8b in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fdb
TitleCrystal Structure of Fibroblast growth factor (FGF)8b in complex with FGF Receptor (FGFR) 2c
Components
  • Fibroblast growth factor receptor 2
  • fibroblast growth factor 8 isoform B
KeywordsHORMONE/GROWTH FACTOR/TRANSFERASE / beta-trefoil fold / immunoglobulin fold / HORMONE-GROWTH FACTOR-TRANSFERASE COMPLEX
Function / homology
Function and homology information


pallium development / midbrain-hindbrain boundary development / negative regulation of cardiac muscle tissue development / subpallium development / larynx morphogenesis / neural plate morphogenesis / type 2 fibroblast growth factor receptor binding / cell migration involved in mesendoderm migration / mitotic nuclear division / mesodermal cell migration ...pallium development / midbrain-hindbrain boundary development / negative regulation of cardiac muscle tissue development / subpallium development / larynx morphogenesis / neural plate morphogenesis / type 2 fibroblast growth factor receptor binding / cell migration involved in mesendoderm migration / mitotic nuclear division / mesodermal cell migration / forebrain dorsal/ventral pattern formation / forebrain neuron development / dorsal/ventral axon guidance / Formation of the posterior neural plate / type 1 fibroblast growth factor receptor binding / embryonic neurocranium morphogenesis / regulation of odontogenesis of dentin-containing tooth / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / 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 / regulation of morphogenesis of a branching structure / gonad development / aorta morphogenesis / orbitofrontal cortex development / cell proliferation in forebrain / epithelial to mesenchymal transition involved in endocardial cushion formation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / endochondral bone growth / morphogenesis of embryonic epithelium / bud elongation involved in lung branching / epidermis morphogenesis / mesonephros development / positive regulation of epithelial cell proliferation involved in lung morphogenesis / reproductive structure development / FGFR3b ligand binding and activation / limb bud formation / membranous septum morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / neuroepithelial cell differentiation / embryonic digestive tract morphogenesis / mesenchymal cell differentiation / forebrain morphogenesis / positive regulation of phospholipase activity / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / epithelial cell proliferation involved in salivary gland morphogenesis / Phospholipase C-mediated cascade; FGFR3 / mesenchymal cell proliferation involved in lung development / branching involved in prostate gland morphogenesis / FGFR2b ligand binding and activation / positive regulation of organ growth / branching involved in labyrinthine layer morphogenesis / lung lobe morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / pharyngeal system development / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / positive regulation of G protein-coupled receptor signaling pathway / fibroblast growth factor receptor activity / FGFR1c ligand binding and activation / organ induction / male genitalia development / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade: FGFR1 / embryonic pattern specification / pyramidal neuron development / embryonic cranial skeleton morphogenesis / lung-associated mesenchyme development / dopaminergic neuron differentiation / metanephros development / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / motor neuron axon guidance / dorsal/ventral pattern formation / mesodermal cell differentiation / bone morphogenesis / embryonic hindlimb morphogenesis
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin domain ...HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 / 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 / Fibroblast growth factor 8 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsMohammadi, M. / Olsen, S.K.
CitationJournal: Genes Dev. / Year: 2006
Title: Structural basis by which alternative splicing modulates the organizer activity of FGF8 in the brain
Authors: Olsen, S.K. / Li, J.Y.H. / Bromleigh, C. / Eliseenkova, A.V. / Ibrahimi, O.A. / Lao, Z. / Zhang, F. / Linhardt, R.J. / Joyner, A.L. / Mohammadi, M.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: fibroblast growth factor 8 isoform B
P: Fibroblast growth factor receptor 2
N: fibroblast growth factor 8 isoform B
R: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)87,3304
Polymers87,3304
Non-polymers00
Water2,252125
1
M: fibroblast growth factor 8 isoform B
P: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)43,6652
Polymers43,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-11 kcal/mol
Surface area16110 Å2
MethodPISA
2
N: fibroblast growth factor 8 isoform B
R: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)43,6652
Polymers43,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-12 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.846, 46.908, 109.616
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number5
Space group name H-MC121
DetailsThere are two biological units. 1) chain A and chain B, and 2) chain C and chain D (i.e. two complexes of FGF8b with FGFR2c

-
Components

#1: Protein fibroblast growth factor 8 isoform B / E.C.2.7.1.112 / FGF8b


Mass: 18906.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P55075
#2: Protein Fibroblast growth factor receptor 2 / FGFR2c / FGFR-2 / Keratinocyte growth factor receptor 2 / CD332 antigen


Mass: 24758.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KSAM / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UQH9, UniProt: P21802*PLUS, EC: 2.7.1.112
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18.5% mPEG 5000, 0.15M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2004
RadiationMonochromator: Kohzu Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 44825 / Num. obs: 44825 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.084 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.8 % / Num. unique all: 4429 / Rsym value: 0.306 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EVT

1evt


Resolution: 2.28→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 6666 15.3 %random
Rwork0.2393 ---
all0.23931 43700 --
obs0.23931 43700 97.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.821 Å20 Å20.672 Å2
2--0.907 Å20 Å2
3---1.728 Å2
Refinement stepCycle: LAST / Resolution: 2.28→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 0 125 5345
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006252
X-RAY DIFFRACTIONc_angle_deg1.3267
X-RAY DIFFRACTIONc_improper_angle_d0.77223
X-RAY DIFFRACTIONc_mcbond_it0.9471.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.4392
X-RAY DIFFRACTIONc_scangle_it2.1222.5

+
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