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- PDB-4cjm: Crystal structure of human FGF18 -

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Basic information

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


type 2 fibroblast growth factor receptor binding / type 1 fibroblast growth factor receptor binding / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / FGFRL1 modulation of FGFR1 signaling / chondrocyte development / intramembranous ossification / positive regulation of chondrocyte differentiation / FGFR3b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 ...type 2 fibroblast growth factor receptor binding / type 1 fibroblast growth factor receptor binding / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / FGFRL1 modulation of FGFR1 signaling / chondrocyte development / intramembranous ossification / positive regulation of chondrocyte differentiation / FGFR3b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR4 ligand binding and activation / endochondral ossification / Phospholipase C-mediated cascade; FGFR4 / positive regulation of vascular endothelial growth factor receptor signaling pathway / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / regulation of cell migration / ERK1 and ERK2 cascade / animal organ morphogenesis / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / lung development / Negative regulation of FGFR4 signaling / growth factor activity / positive regulation of MAP kinase activity / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / cell population proliferation / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / signal transduction / extracellular space / extracellular region / 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 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

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

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Components

#1: Protein
FIBROBLAST GROWTH FACTOR 18 / 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


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


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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