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- PDB-5vak: Crystal Structure of Beta-Klotho, Domain 1 -

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Basic information

Entry
Database: PDB / ID: 5vak
TitleCrystal Structure of Beta-Klotho, Domain 1
Components
  • Beta-klotho
  • Nb914
KeywordsSIGNALING PROTEIN / (beta/alpha)8
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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 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
Revision 2.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Nb914
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0804
Polymers71,4342
Non-polymers6462
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint2 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.427, 49.346, 54.306
Angle α, β, γ (deg.)90.000, 100.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 56597.031 Da / Num. of mol.: 1 / Fragment: UNP residies 30-522
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: 30% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1808 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 1.7→48.208 Å / Num. obs: 65245 / % possible obs: 98 % / Redundancy: 4.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.36
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.87 / Num. unique obs: 5637 / % possible all: 87

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.208 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.19
RfactorNum. reflection% reflection
Rfree0.1964 3168 4.86 %
Rwork0.1717 --
obs0.1729 65180 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.89 Å2 / Biso mean: 26.5625 Å2 / Biso min: 13.46 Å2
Refinement stepCycle: final / Resolution: 1.7→48.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4453 0 42 271 4766
Biso mean--45.67 30.97 -
Num. residues----558

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