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- PDB-5van: Crystal Structure of Beta-Klotho -

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Basic information

Entry
Database: PDB / ID: 5van
TitleCrystal Structure of Beta-Klotho
Components
  • Beta-klotho
  • Nb914
KeywordsSIGNALING PROTEIN / (beta/alpha)8 Receptor for Endocrine FGF
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
beta-D-glucopyranose / alpha-D-mannopyranose / Beta-klotho
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 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: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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

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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)126,43611
Polymers124,4322
Non-polymers2,0049
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint15 kcal/mol
Surface area38220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.683, 144.069, 215.612
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein 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

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Sugars , 4 types, 8 molecules

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 113 molecules

#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
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: SSRL / Beamline: BL14-1 / Wavelength: 1.1808 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: May 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 2.202→47.488 Å / Num. obs: 77797 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1093 / Net I/σ(I): 20.13
Reflection shellResolution: 2.202→2.281 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.8798 / Mean I/σ(I) obs: 2.71 / Num. unique obs: 7442 / CC1/2: 0.763 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.202→47.488 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2107 3890 5 %
Rwork0.1862 --
obs0.1874 77784 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.41 Å2 / Biso mean: 43.3013 Å2 / Biso min: 22.99 Å2
Refinement stepCycle: final / Resolution: 2.202→47.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7731 0 125 112 7968
Biso mean--65.37 39.59 -
Num. residues----983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088087
X-RAY DIFFRACTIONf_angle_d0.94311001
X-RAY DIFFRACTIONf_chiral_restr0.0531191
X-RAY DIFFRACTIONf_plane_restr0.0061381
X-RAY DIFFRACTIONf_dihedral_angle_d14.0724665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2017-2.22850.26521280.25112364249291
2.2285-2.25670.26731350.252225902725100
2.2567-2.28640.26571330.239526082741100
2.2864-2.31780.23481300.233226442774100
2.3178-2.35090.27611230.236126072730100
2.3509-2.3860.24471450.233125822727100
2.386-2.42320.27651330.229726642797100
2.4232-2.4630.2471360.219925792715100
2.463-2.50540.27351350.214426152750100
2.5054-2.5510.27551400.218126412781100
2.551-2.60010.30281400.214825962736100
2.6001-2.65310.25031500.209326022752100
2.6531-2.71080.2291460.211726732819100
2.7108-2.77390.24151340.221225902724100
2.7739-2.84320.2561240.211626562780100
2.8432-2.92010.27461470.214926062753100
2.9201-3.0060.25351350.212626402775100
3.006-3.1030.22291490.208426482797100
3.103-3.21390.20991470.202826412788100
3.2139-3.34250.24491390.197626382777100
3.3425-3.49460.21091320.186726682800100
3.4946-3.67880.18071580.177626192777100
3.6788-3.90920.19091430.159326712814100
3.9092-4.21080.1951400.151326772817100
4.2108-4.63430.16641340.139927032837100
4.6343-5.30410.18591480.147627242872100
5.3041-6.67960.16041360.185427472883100
6.6796-47.49860.1751500.180129013051100

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