[English] 日本語
Yorodumi
- PDB-4qbc: Crystal structure of C117T mutant of human acidic fibroblast grow... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qbc
TitleCrystal structure of C117T mutant of human acidic fibroblast growth factor in sodium formate buffer
ComponentsFibroblast growth factor 1
KeywordsPROTEIN BINDING / Beta-trefoil / growth factor / FGFR binding / heparin binding
Function / homology
Function and homology information


mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / 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 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / S100 protein binding / positive regulation of hepatocyte proliferation / PI-3K cascade:FGFR3 / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of sprouting angiogenesis / positive regulation of intracellular signal transduction / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / activation of protein kinase B activity / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / positive regulation of MAP kinase activity / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / neurogenesis / Signaling by FGFR1 in disease / extracellular matrix / positive regulation of endothelial cell migration / Hsp70 protein binding / regulation of cell migration / epithelial cell proliferation / Negative regulation of FGFR3 signaling / growth factor activity / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / lung development / Negative regulation of FGFR1 signaling / wound healing / positive regulation of cholesterol biosynthetic process / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / heparin binding / cellular response to heat / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell cortex / angiogenesis / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell migration / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.519 Å
AuthorsBlaber, M. / Xia, X.
CitationJournal: J.Pharm.Sci. / Year: 2015
Title: Mutation choice to eliminate buried free cysteines in protein therapeutics.
Authors: Xia, X. / Longo, L.M. / Blaber, M.
History
DepositionMay 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibroblast growth factor 1
B: Fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6507
Polymers33,3692
Non-polymers2805
Water7,386410
1
A: Fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8273
Polymers16,6851
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroblast growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8234
Polymers16,6851
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.735, 95.377, 106.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Fibroblast growth factor 1 / FGF-1 / Acidic fibroblast growth factor / aFGF / Endothelial cell growth factor / ECGF / Heparin- ...FGF-1 / Acidic fibroblast growth factor / aFGF / Endothelial cell growth factor / ECGF / Heparin-binding growth factor 1 / HBGF-1


Mass: 16684.709 Da / Num. of mol.: 2 / Fragment: UNP residues 16-155 / Mutation: C117T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05230
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4.0 M sodium formate, 0.45 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97911 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2014
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.519→50 Å / Num. obs: 57173 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.4 %
Reflection shellHighest resolution: 1.519 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(Phaser MR)model building
PHENIX(phenix.refine: 1.9_1690)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(Phaser MR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.519→30.266 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 18.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 2000 3.5 %
Rwork0.1699 --
obs0.1709 57131 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.519→30.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 17 410 2711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112405
X-RAY DIFFRACTIONf_angle_d1.1723254
X-RAY DIFFRACTIONf_dihedral_angle_d14.116904
X-RAY DIFFRACTIONf_chiral_restr0.046336
X-RAY DIFFRACTIONf_plane_restr0.005425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.519-1.55740.23761370.19713776X-RAY DIFFRACTION97
1.5574-1.59950.21151420.19243900X-RAY DIFFRACTION100
1.5995-1.64660.21961420.19193918X-RAY DIFFRACTION100
1.6466-1.69970.2151420.18763926X-RAY DIFFRACTION100
1.6997-1.76040.19871420.18533902X-RAY DIFFRACTION100
1.7604-1.83090.18321420.1783901X-RAY DIFFRACTION100
1.8309-1.91420.21751420.17293938X-RAY DIFFRACTION100
1.9142-2.01510.19421430.1793933X-RAY DIFFRACTION100
2.0151-2.14140.19851430.16773956X-RAY DIFFRACTION100
2.1414-2.30660.17181430.17053935X-RAY DIFFRACTION100
2.3066-2.53870.19131430.18063937X-RAY DIFFRACTION100
2.5387-2.90580.18111440.17333974X-RAY DIFFRACTION100
2.9058-3.65990.20171460.15694002X-RAY DIFFRACTION100
3.6599-30.27230.21051490.15524133X-RAY DIFFRACTION99

+
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