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- PDB-5wi9: Crystal structure of KL with an agonist Fab -

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Basic information

Entry
Database: PDB / ID: 5wi9
TitleCrystal structure of KL with an agonist Fab
Components
  • 39F7 Fab heavy chain
  • 39F7 Fab light chain
  • Beta-klotho
KeywordsSTRUCTURAL PROTEIN / beta-klotho / scaffold protein / fibroblast growth factors
Function / homology
Function and homology information


betaKlotho-mediated ligand binding / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / fibroblast growth factor receptor binding / Phospholipase C-mediated cascade; FGFR4 / fibroblast growth factor binding / PI-3K cascade:FGFR4 / PI3K Cascade / SHC-mediated cascade:FGFR4 / hydrolase activity, hydrolyzing O-glycosyl compounds / FRS-mediated FGFR4 signaling ...betaKlotho-mediated ligand binding / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / fibroblast growth factor receptor binding / Phospholipase C-mediated cascade; FGFR4 / fibroblast growth factor binding / PI-3K cascade:FGFR4 / PI3K Cascade / SHC-mediated cascade:FGFR4 / hydrolase activity, hydrolyzing O-glycosyl compounds / FRS-mediated FGFR4 signaling / Negative regulation of FGFR4 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / carbohydrate metabolic process / positive regulation of cell population proliferation / plasma membrane
Similarity search - Function
Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJohnstone, S. / Min, X. / Wang, Z.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Agonistic beta-Klotho antibody mimics fibroblast growth factor 21 (FGF21) functions.
Authors: Min, X. / Weiszmann, J. / Johnstone, S. / Wang, W. / Yu, X. / Romanow, W. / Thibault, S. / Li, Y. / Wang, Z.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
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 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-klotho
B: Beta-klotho
L: 39F7 Fab light chain
H: 39F7 Fab heavy chain
E: 39F7 Fab light chain
F: 39F7 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,53421
Polymers203,6346
Non-polymers1,90015
Water2,810156
1
A: Beta-klotho
L: 39F7 Fab light chain
H: 39F7 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,11614
Polymers101,8173
Non-polymers1,29911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-4 kcal/mol
Surface area33320 Å2
MethodPISA
2
B: Beta-klotho
E: 39F7 Fab light chain
F: 39F7 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4187
Polymers101,8173
Non-polymers6014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-31 kcal/mol
Surface area34070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.018, 68.465, 147.811
Angle α, β, γ (deg.)90.000, 111.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules LEHF

#2: Antibody 39F7 Fab light chain


Mass: 23240.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 39F7 Fab heavy chain


Mass: 24111.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 6 molecules AB

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


Mass: 54465.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLB / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q86Z14
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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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Non-polymers , 4 types, 167 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M sodium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 60307 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.095 / Rrim(I) all: 0.185 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.77 / CC1/2: 0.617 / Rpim(I) all: 0.547 / Rrim(I) all: 1.073 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.88 / SU B: 16.136 / SU ML: 0.313 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.2 / ESU R Free: 0.361
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 2979 4.9 %RANDOM
Rwork0.2156 ---
obs0.2183 57323 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.53 Å2 / Biso mean: 47.553 Å2 / Biso min: 8 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å2-1.81 Å2
2--3.55 Å2-0 Å2
3----2.78 Å2
Refinement stepCycle: final / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13280 0 120 156 13556
Biso mean--57.51 26.92 -
Num. residues----1680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01913773
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212650
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.93818682
X-RAY DIFFRACTIONr_angle_other_deg1.025329121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.59851667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95823.659615
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.968152163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5491565
X-RAY DIFFRACTIONr_chiral_restr0.0780.22001
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115501
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023346
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 192 -
Rwork0.319 4221 -
all-4413 -
obs--99.32 %

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