[English] 日本語
Yorodumi
- PDB-2ki6: The FGF1-S100A13-C2A hetero-hexameric complex structure: A compon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ki6
TitleThe FGF1-S100A13-C2A hetero-hexameric complex structure: A component in the non-classical pathway for FGF1 secretion
Components
  • (Protein S100-A13) x 2
  • Heparin-binding growth factor 1
  • Synaptotagmin-1
KeywordsPROTEIN TRANSPORT / FGF1-S100A13-C2A hetero-hexameric complex / FGF1 / S100A13 / C2A / Calcium / Cell junction / Cytoplasmic vesicle / Glycoprotein / Lipoprotein / Membrane / Metal-binding / Palmitate / Phosphoprotein / Synapse / Transmembrane / Acetylation / Alternative splicing / Angiogenesis / Developmental protein / Differentiation / Growth factor / Heparin-binding / Mitogen / Polymorphism
Function / homology
Function and homology information


clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / Toxicity of botulinum toxin type B (botB) ...clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / chromaffin granule membrane / dense core granule / 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 / positive regulation of interleukin-1 alpha production / regulation of endothelial tube morphogenesis / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / Serotonin Neurotransmitter Release Cycle / FGFR3b ligand binding and activation / vesicle docking / regulation of endothelial cell chemotaxis to fibroblast growth factor / exocytic vesicle / regulation of exocytosis / RAGE receptor binding / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / vesicle organization / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / protein heterooligomerization / vesicle fusion / positive regulation of dopamine secretion / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / Glutamate Neurotransmitter Release Cycle / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / positive regulation of dendrite extension / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / S100 protein binding / positive regulation of hepatocyte proliferation / syntaxin-1 binding / Neurexins and neuroligins / clathrin binding / low-density lipoprotein particle receptor binding / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / mast cell degranulation / regulation of synaptic vesicle exocytosis / phosphatidylserine binding / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of sprouting angiogenesis / fibroblast growth factor binding / positive regulation of intracellular signal transduction / presynaptic active zone / positive regulation of cell division / postsynaptic cytosol / excitatory synapse / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / detection of calcium ion / positive regulation of synaptic transmission / SHC-mediated cascade:FGFR3 / presynaptic cytosol / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / regulation of synaptic transmission, glutamatergic / activation of protein kinase B activity / FRS-mediated FGFR3 signaling / vesicle-mediated transport / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / neurogenesis / Signaling by FGFR2 in disease / phosphatidylinositol-4,5-bisphosphate binding
Similarity search - Function
Synaptotagmin / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Cytokine IL1/FGF / C2 domain ...Synaptotagmin / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / 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 / EF-hand / Recoverin; domain 1 / C2 domain superfamily / EF-hand domain pair / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Fibroblast growth factor 1 / Synaptotagmin-1 / Protein S100-A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsKrishna, S.M. / Rani, S.G. / Yu, C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The heterohexameric complex structure, a component in the non-classical pathway for fibroblast growth factor 1 (FGF1) secretion.
Authors: Mohan, S.K. / Rani, S.G. / Yu, C.
History
DepositionApr 28, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptotagmin-1
B: Heparin-binding growth factor 1
C: Protein S100-A13
D: Protein S100-A13
E: Heparin-binding growth factor 1
F: Synaptotagmin-1


Theoretical massNumber of molelcules
Total (without water)82,7816
Polymers82,7816
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)18 / 2000structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

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


Mass: 14783.882 Da / Num. of mol.: 2 / Fragment: C2A domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: purified from heparin affinity column / 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: purified from GST column / Gene: FGF1, FGFA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05230
#3: Protein Protein S100-A13 / S100 calcium-binding protein A13


Mass: 11488.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: purified from GST column / Gene: S100A13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99584
#4: Protein Protein S100-A13 / S100 calcium-binding protein A13


Mass: 11489.187 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: purified from GST column / Gene: S100A13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99584
Has protein modificationN
Sequence detailsTHE CHAIN C AND D ARE S100A13 MONOMERS; BUT IN CHAIN C AND D THE 94, 97 AND 98 RESIDUES ARE ...THE CHAIN C AND D ARE S100A13 MONOMERS; BUT IN CHAIN C AND D THE 94, 97 AND 98 RESIDUES ARE DIFFERENT ISOMERS (DLY OR LYS).

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: The FGF1-S100A13-C2A hetero-hexameric complex structure
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D-13C-filter NOESY
11213D-15N-filter NOESY
11313D H(CCO)NH
NMR detailsText: C2A(15N&13C labeled) mixed with unlabeled FGF1-S100A13 complex buffer condition (25mM PBD, 100mM NaCl and 2mM CaCl2)

-
Sample preparation

DetailsContents: 1.0mM [U-100% 13C; U-100% 15N] C2A domain of Syt1-1, 1.0mM FGF1-2, 1.0mM S100A13-3, S100A13-4, 25mM sodium phosphate-5, 100mM sodium chloride-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMC2A domain of Syt1-1[U-100% 13C; U-100% 15N]1
1.0 mMFGF1-21
1.0 mMS100A13-31
1.0 mMS100A13-41
25 mMsodium phosphate-51
100 mMsodium chloride-61
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2 &2.2Linge, O'Donoghue and Nilgesstructure solution
CNSSOLVE1.1 & 1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSSOLVE1.1 & 1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 2000 / Conformers submitted total number: 18 / 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