[English] 日本語
Yorodumi
- PDB-2q9x: Crystal structure of highly stable mutant Q40P/S47I/H93G of human... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q9x
TitleCrystal structure of highly stable mutant Q40P/S47I/H93G of human fibroblast growth factor-1
ComponentsHeparin-binding growth factor 1
KeywordsHORMONE / FGF-1 / growth factor / beta trefoil / enhanced stability
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 / positive regulation of cholesterol biosynthetic process ...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 / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / 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 / organ induction / FGFR1c ligand binding and activation / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / S100 protein binding / positive regulation of hepatocyte proliferation / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / 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 / Signaling by FGFR1 in disease / Hsp70 protein binding / regulation of cell migration / activation of protein kinase B activity / positive regulation of endothelial cell migration / extracellular matrix / epithelial cell proliferation / animal organ morphogenesis / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / lung development / Negative regulation of FGFR1 signaling / positive regulation of MAP kinase activity / growth factor activity / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / heparin binding / cellular response to heat / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / 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
Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSzlachcic, A. / Zakrzewska, M. / Krowarsch, D. / Os, V. / Helland, R. / Otlewski, J.
CitationJournal: To be Published
Title: Crystal structure of highly stable mutant Q40P/S47I/H93G of human fibroblast growth factor-1
Authors: Szlachcic, A. / Zakrzewska, M. / Krowarsch, D. / Os, V. / Helland, R. / Otlewski, J.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8642
Polymers15,7721
Non-polymers921
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.610, 57.599, 57.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL ASSEMBLY IS A MONOMER

-
Components

#1: Protein Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / aFGF / Beta-endothelial cell growth factor / ECGF- beta


Mass: 15771.837 Da / Num. of mol.: 1 / Mutation: Q40P, S47I, H93G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P05230
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.82 Å3/Da / Density % sol: 32.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 8000, 100mM TrisHCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.8698 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8698 Å / Relative weight: 1
ReflectionResolution: 1.6→34.61 Å / Num. all: 15833 / Num. obs: 13265 / % possible obs: 100 % / Redundancy: 4 % / Biso Wilson estimate: 11.93 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 5.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 1.9 / Num. measured all: 7487 / Num. unique all: 1866 / Rsym value: 0.356 / % possible all: 100

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å29.68 Å
Translation1.8 Å29.68 Å

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RG8

1rg8


Resolution: 1.7→34.6 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / SU B: 2.572 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 651 4.9 %RANDOM
Rwork0.207 ---
all0.208 15833 --
obs0.209 13212 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.686 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1007 0 6 107 1120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221033
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9761393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4215126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93824.16748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67115180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.545156
X-RAY DIFFRACTIONr_chiral_restr0.1120.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02780
X-RAY DIFFRACTIONr_nbd_refined0.2090.2452
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2665
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.29
X-RAY DIFFRACTIONr_mcbond_it0.9591.5651
X-RAY DIFFRACTIONr_mcangle_it1.49821009
X-RAY DIFFRACTIONr_scbond_it2.2163439
X-RAY DIFFRACTIONr_scangle_it3.1914.5384
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 43 -
Rwork0.259 906 -
obs-949 100 %

+
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