[English] 日本語
Yorodumi
- PDB-1pwa: Crystal structure of Fibroblast Growth Factor 19 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pwa
TitleCrystal structure of Fibroblast Growth Factor 19
ComponentsFibroblast growth factor-19
KeywordsHORMONE/GROWTH FACTOR / BETA TREFOIL / DISULPHIDE BONDS / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling ...negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling / regulation of cell migration / positive regulation of glucose import / Negative regulation of FGFR4 signaling / positive regulation of JNK cascade / animal organ morphogenesis / growth factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cell differentiation / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Fibroblast growth factor 15/19/21 / 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 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHarmer, N.J. / Pellegrini, L. / Chirgadze, D. / Fernandez-Recio, J. / Blundell, T.L.
CitationJournal: Biochemistry / Year: 2004
Title: The crystal structure of fibroblast growth factor (FGF) 19 reveals novel features of the FGF family and offers a structural basis for its unusual receptor affinity.
Authors: Harmer, N.J. / Pellegrini, L. / Chirgadze, D. / Fernandez-Recio, J. / Blundell, T.L.
History
DepositionJul 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 16, 2014Group: Data collection
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4274
Polymers18,1171
Non-polymers3103
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.573, 67.573, 193.374
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-239-

HOH

21A-304-

HOH

31A-362-

HOH

-
Components

#1: Protein Fibroblast growth factor-19 / FGF-19


Mass: 18116.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF19 / Plasmid: pGAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: O95750
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, potassium phosphate, magnesium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMTris-HCl1drop
2200 mM1dropNaCl
312-14 %(w/w)PEG33501reservoir
40.25 M1reservoirMgSO4
50.1 Mpotassium phosphate1reservoirpH7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 16, 2003 / Details: mirrors
RadiationMonochromator: Rh coated silica / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. all: 42313 / % possible obs: 99.9 % / Redundancy: 12.08 % / Biso Wilson estimate: 13.695 Å2 / Rsym value: 0.062 / Net I/σ(I): 36.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 4.32 / Num. unique all: 2080 / Rsym value: 0.586 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 23.33 Å / Num. obs: 42303 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 4.33

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1JQZ, 2FGF, 1IJT, 1QQK, 1IHK

1jqz

2fgf

1ijt

1qqk

1ihk


Resolution: 1.3→23.33 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 0.508 / SU ML: 0.022 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 2058 -RANDOM
Rwork0.1798 ---
all0.1807 ---
obs0.1807 42303 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.373 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.046 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.3→23.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 19 267 1236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211032
X-RAY DIFFRACTIONr_bond_other_d0.0040.02958
X-RAY DIFFRACTIONr_angle_refined_deg1.4372.0031395
X-RAY DIFFRACTIONr_angle_other_deg1.0532243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245121
X-RAY DIFFRACTIONr_chiral_restr0.0990.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021093
X-RAY DIFFRACTIONr_gen_planes_other0.010.02196
X-RAY DIFFRACTIONr_nbd_refined0.230.2174
X-RAY DIFFRACTIONr_nbd_other0.2780.21172
X-RAY DIFFRACTIONr_nbtor_other0.0840.2598
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2660.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.245
X-RAY DIFFRACTIONr_mcbond_it1.2441.5629
X-RAY DIFFRACTIONr_mcangle_it1.9721024
X-RAY DIFFRACTIONr_scbond_it2.2583403
X-RAY DIFFRACTIONr_scangle_it3.554.5371
X-RAY DIFFRACTIONr_rigid_bond_restr1.29121032
X-RAY DIFFRACTIONr_sphericity_free4.1082267
X-RAY DIFFRACTIONr_sphericity_bonded2.95421012
LS refinement shellResolution: 1.298→1.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 148 -
Rwork0.19 3054 -
obs-2906 100 %
Refinement
*PLUS
Highest resolution: 1.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.44

+
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://pdbjlvh1.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