[English] 日本語
Yorodumi
- PDB-2k4a: FGF-1-C2A binary complex structure: a key component in the fibrob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k4a
TitleFGF-1-C2A binary complex structure: a key component in the fibroblast growthfactor non-classical pathway
Components
  • Heparin-binding growth factor 1
  • Synaptotagmin-1
KeywordsPROTEIN TRANSPORT / beta barrel / FGF1-C2A binary complex / Calcium / Cell junction / Cytoplasmic vesicle / Glycoprotein / Lipoprotein / Membrane / Metal-binding / Palmitate / Phosphoprotein / Synapse / Transmembrane / Acetylation / Angiogenesis / Developmental protein / Differentiation / Growth factor / Heparin-binding / Mitogen / Polymorphism
Function / homology
Function and homology information


Toxicity of botulinum toxin type G (botG) / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane ...Toxicity of botulinum toxin type G (botG) / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / GABA synthesis, release, reuptake and degradation / Acetylcholine Neurotransmitter Release Cycle / mesonephric epithelium development / branch elongation involved in ureteric bud branching / clathrin-sculpted monoamine transport vesicle membrane / regulation of endothelial tube morphogenesis / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / Serotonin Neurotransmitter Release Cycle / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / exocytic vesicle / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / vesicle organization / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / protein heterooligomerization / Phospholipase C-mediated cascade; FGFR3 / positive regulation of dendrite extension / FGFR2b ligand binding and activation / vesicle docking / fibroblast growth factor receptor binding / regulation of exocytosis / Glutamate Neurotransmitter Release Cycle / positive regulation of dopamine secretion / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / vesicle fusion / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / dense core granule / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / neurotransmitter secretion / S100 protein binding / presynaptic active zone / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / Signaling by FGFR2 IIIa TM / clathrin binding / PI-3K cascade:FGFR3 / phosphatidylserine binding / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of sprouting angiogenesis / regulation of synaptic vesicle exocytosis / positive regulation of MAP kinase activity / positive regulation of intracellular signal transduction / positive regulation of cell division / PI3K Cascade / excitatory synapse / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / activation of protein kinase B activity / detection of calcium ion / positive regulation of synaptic transmission / postsynaptic cytosol / SHC-mediated cascade:FGFR3 / regulation of synaptic transmission, glutamatergic / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / presynaptic cytosol / FRS-mediated FGFR3 signaling / vesicle-mediated transport / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / neurogenesis / Signaling by FGFR2 in disease / phosphatidylinositol-4,5-bisphosphate binding / Signaling by FGFR1 in disease / extracellular matrix / positive regulation of endothelial cell migration / lung development
Similarity search - Function
Synaptotagmin / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain ...Synaptotagmin / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 1 / Synaptotagmin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYu, C. / Mohan, S.K.
CitationJournal: To be Published
Title: FGF-1-C2A binary complex structure: key component in the acidic fibroblast growth factor release
Authors: Mohan, S.K. / Yu, C.
History
DepositionJun 2, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptotagmin-1
B: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)29,9022
Polymers29,9022
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Synaptotagmin-1 / Synaptotagmin I / SytI / p65 / C2A


Mass: 14783.882 Da / Num. of mol.: 1 / Fragment: C2 domain, UNP residues 141-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYT1, SVP65, SYT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Protein Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / aFGF / Beta-endothelial cell growth factor / ECGF-beta


Mass: 15118.044 Da / Num. of mol.: 1 / Fragment: UNP residues 23-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05230

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 13C(w2)-edited 12C(w2)-filtered NOESY

-
Sample preparation

DetailsContents: 1.2mM FGF-1-C2A; 100% D2O / Solvent system: 100% D2O
SampleConc.: 1.2 mM / Component: FGF-1-C2A
Sample conditionsIonic strength: 50mM (NH4)2SO4 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AV800BrukerAV8008001
Bruker AV800BrukerAV80080013C-filter-NOESY

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue, Nilgesstructure solution
HADDOCK2Alexandre Bonvinstructure solution
SparkyGoddardchemical shift assignment
TopSpin1.3Bruker Biospinprocessing
TALOSCornilescu, Delaglio, Baxfor dihedrals
HADDOCK2Alexandre Bonvinrefinement
ARIA/CNSBRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON,WARRENrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: HADDOCK
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 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