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- PDB-5vaq: Crystal Structure of Beta-Klotho in Complex with FGF21CT -

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Basic information

Entry
Database: PDB / ID: 5vaq
TitleCrystal Structure of Beta-Klotho in Complex with FGF21CT
Components
  • Beta-klotho
  • Fibroblast growth factor 21
  • Nb914
KeywordsSIGNALING PROTEIN / (beta/alpha) 8 Receptor for Endocrine FGF
Function / homology
Function and homology information


positive regulation of triglyceride catabolic process / Cellular hexose transport / betaKlotho-mediated ligand binding / response to methionine / Assembly of active LPL and LIPC lipase complexes / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of low-density lipoprotein particle clearance / fibroblast growth factor receptor binding / Phospholipase C-mediated cascade; FGFR4 / endothelial cell apoptotic process ...positive regulation of triglyceride catabolic process / Cellular hexose transport / betaKlotho-mediated ligand binding / response to methionine / Assembly of active LPL and LIPC lipase complexes / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of low-density lipoprotein particle clearance / fibroblast growth factor receptor binding / Phospholipase C-mediated cascade; FGFR4 / endothelial cell apoptotic process / positive regulation of low-density lipoprotein receptor activity / fibroblast growth factor binding / PI-3K cascade:FGFR4 / cellular response to glucagon stimulus / cellular response to low-density lipoprotein particle stimulus / PI3K Cascade / fibroblast growth factor receptor signaling pathway / negative regulation of endothelial cell apoptotic process / SHC-mediated cascade:FGFR4 / endoplasmic reticulum unfolded protein response / regulation of cell migration / hydrolase activity, hydrolyzing O-glycosyl compounds / FRS-mediated FGFR4 signaling / response to nutrient levels / response to activity / positive regulation of glucose import / cellular response to glucose stimulus / Negative regulation of FGFR4 signaling / animal organ morphogenesis / growth factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / cellular response to xenobiotic stimulus / PIP3 activates AKT signaling / cell-cell signaling / positive regulation of cold-induced thermogenesis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / carbohydrate metabolic process / 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 / signal transduction / extracellular space / extracellular region / plasma membrane / 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 / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily ...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 / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Beta-klotho / Fibroblast growth factor 21
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.606 Å
AuthorsLee, S. / Schlessinger, J.
CitationJournal: Nature / Year: 2018
Title: Structures of beta-klotho reveal a 'zip code'-like mechanism for endocrine FGF signalling.
Authors: Lee, S. / Choi, J. / Mohanty, J. / Sousa, L.P. / Tome, F. / Pardon, E. / Steyaert, J. / Lemmon, M.A. / Lax, I. / Schlessinger, J.
History
DepositionMar 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-klotho
B: Nb914
C: Fibroblast growth factor 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0514
Polymers126,8293
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.647, 145.487, 213.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Beta-klotho / BetaKlotho / Klotho beta-like protein


Mass: 109594.398 Da / Num. of mol.: 1 / Fragment: UNP residues30-983 / Mutation: N308Q, N611Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLB / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q86Z14
#2: Antibody Nb914


Mass: 14837.451 Da / Num. of mol.: 1 / Fragment: Nanobody
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Antibody Fibroblast growth factor 21 / / FGF-21


Mass: 2397.512 Da / Num. of mol.: 1 / Fragment: UNP residues 186-209 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NSA1
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6 / Details: 14% PEG 4000, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.606→64.007 Å / Num. obs: 46776 / % possible obs: 98 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09048 / Net I/σ(I): 13.12

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.606→64.007 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26
RfactorNum. reflection% reflection
Rfree0.229 2325 5 %
Rwork0.1911 --
obs0.193 46522 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.46 Å2 / Biso mean: 63.4244 Å2 / Biso min: 37.72 Å2
Refinement stepCycle: final / Resolution: 2.606→64.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7874 0 13 0 7887
Biso mean--68.9 --
Num. residues----1005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128120
X-RAY DIFFRACTIONf_angle_d1.28711035
X-RAY DIFFRACTIONf_chiral_restr0.0661173
X-RAY DIFFRACTIONf_plane_restr0.0081399
X-RAY DIFFRACTIONf_dihedral_angle_d14.9164682
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6061-2.65930.3931240.3592270239488
2.6593-2.71710.36861220.32412590271298
2.7171-2.78030.34021400.3042564270499
2.7803-2.84980.36571280.27252631275999
2.8498-2.92690.30591370.27252568270599
2.9269-3.0130.29221590.255326172776100
3.013-3.11030.30081220.25092605272799
3.1103-3.22140.25971310.2312646277799
3.2214-3.35040.30311510.21432552270399
3.3504-3.50290.24461370.20112662279999
3.5029-3.68750.25251210.19122614273599
3.6875-3.91850.21041380.17532602274099
3.9185-4.2210.20051330.15052613274698
4.221-4.64570.16821370.13772641277898
4.6457-5.31770.17991400.14642659279998
5.3177-6.69860.21891600.17682629278997
6.6986-64.02640.18981450.17912734287995

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