[English] 日本語
Yorodumi
- PDB-4cjm: Crystal structure of human FGF18 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cjm
TitleCrystal structure of human FGF18
ComponentsFIBROBLAST GROWTH FACTOR 18FGF18
KeywordsSIGNALING PROTEIN / SIGNALLING
Function / homology
Function and homology information


FGFR3 mutant receptor activation / type 2 fibroblast growth factor receptor binding / : / type 1 fibroblast growth factor receptor binding / FGFRL1 modulation of FGFR1 signaling / chondrocyte development / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of chondrocyte differentiation / intramembranous ossification / FGFR3b ligand binding and activation ...FGFR3 mutant receptor activation / type 2 fibroblast growth factor receptor binding / : / type 1 fibroblast growth factor receptor binding / FGFRL1 modulation of FGFR1 signaling / chondrocyte development / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of chondrocyte differentiation / intramembranous ossification / FGFR3b ligand binding and activation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / endochondral ossification / positive regulation of vascular endothelial growth factor receptor signaling pathway / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI3K Cascade / anatomical structure morphogenesis / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR2 in disease / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / lung development / growth factor activity / positive regulation of MAP kinase activity / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / cell-cell signaling / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell population proliferation / nucleolus / signal transduction / extracellular space / extracellular region
Similarity search - Function
Fibroblast growth factor 18 / 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 18
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBrown, A. / Adam, L.E. / Blundell, T.L.
CitationJournal: Protein Cell / Year: 2014
Title: The Crystal Structure of Fibroblast Growth Factor 18 (Fgf18)
Authors: Brown, A. / Adam, L.E. / Blundell, T.L.
History
DepositionDec 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Feb 28, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FIBROBLAST GROWTH FACTOR 18
B: FIBROBLAST GROWTH FACTOR 18
C: FIBROBLAST GROWTH FACTOR 18
D: FIBROBLAST GROWTH FACTOR 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,74517
Polymers65,4964
Non-polymers1,24913
Water1448
1
A: FIBROBLAST GROWTH FACTOR 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7585
Polymers16,3741
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIBROBLAST GROWTH FACTOR 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6624
Polymers16,3741
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FIBROBLAST GROWTH FACTOR 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5663
Polymers16,3741
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FIBROBLAST GROWTH FACTOR 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7585
Polymers16,3741
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.760, 49.496, 100.854
Angle α, β, γ (deg.)90.00, 101.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA51 - 1772 - 128
21ARGARGBB51 - 1772 - 128
12ARGARGAA51 - 1772 - 128
22ARGARGCC51 - 1772 - 128
13ARGARGAA51 - 1772 - 128
23ARGARGDD51 - 1772 - 128
14TYRTYRBB51 - 1782 - 129
24TYRTYRCC51 - 1782 - 129
15ARGARGBB51 - 1772 - 128
25ARGARGDD51 - 1772 - 128
16ARGARGCC51 - 1772 - 128
26ARGARGDD51 - 1772 - 128

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
FIBROBLAST GROWTH FACTOR 18 / FGF18 / FGF-18 / ZFGF5


Mass: 16373.931 Da / Num. of mol.: 4 / Fragment: RESIDUES 50-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PBAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-GAMI2 / References: UniProt: O76093
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.5, 0.2 M (NH4)2SO4 AND 26% PEG 5000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Details: HELIOS MX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→98.74 Å / Num. obs: 17815 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 19.3 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 15.84
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 12.99 % / Mean I/σ(I) obs: 2.83 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PROTEUM2data reduction
PROTEUM2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FDB

2fdb


Resolution: 2.7→98.74 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.875 / SU B: 26.936 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25083 907 5.1 %RANDOM
Rwork0.21155 ---
obs0.21344 16899 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.362 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å21.47 Å2
2---0.04 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.7→98.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 65 8 4261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194325
X-RAY DIFFRACTIONr_bond_other_d0.0050.024180
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.985783
X-RAY DIFFRACTIONr_angle_other_deg1.13139613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52522.549204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21115844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4561544
X-RAY DIFFRACTIONr_chiral_restr0.0720.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024759
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021045
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2331.0712052
X-RAY DIFFRACTIONr_mcbond_other1.2261.072051
X-RAY DIFFRACTIONr_mcangle_it2.0371.5982558
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3531.4322273
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A77170.1
12B77170.1
21A76340.1
22C76340.1
31A75400.11
32D75400.11
41B76920.1
42C76920.1
51B76190.1
52D76190.1
61C76980.1
62D76980.1
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 57 -
Rwork0.29 1243 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7686-0.2626-0.1943.39880.1723.9498-0.0061-0.12770.0310.0730.007-0.1004-0.0041-0.014-0.00090.21260.0089-0.0120.0064-0.00080.0202-1.041-11.7129.376
22.67680.27060.013.54770.0074.3534-0.06350.2683-0.06420.00860.0107-0.0040.0144-0.17220.05270.2581-0.03450.06450.0457-0.03620.0666-12.09-9.86440.146
32.67260.5343-0.04495.80940.03553.66710.03120.25510.0122-0.38280.00090.11470.1249-0.1702-0.0320.3493-0.00670.02270.04920.02970.198420.9253.71740.189
43.4001-0.5354-1.10185.1725-0.10564.1986-0.0088-0.2468-0.11370.3863-0.01910.05850.0709-0.00380.02790.25130.00060.00110.02170.01940.147530.574-26.4669.178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A51 - 179
2X-RAY DIFFRACTION2B51 - 178
3X-RAY DIFFRACTION3C51 - 178
4X-RAY DIFFRACTION4D50 - 178

+
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