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- PDB-3sob: The structure of the first YWTD beta propeller domain of LRP6 in ... -

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Basic information

Entry
Database: PDB / ID: 3sob
TitleThe structure of the first YWTD beta propeller domain of LRP6 in complex with a FAB
Components
  • Low-density lipoprotein receptor-related protein 6
  • antibody heavy chainImmunoglobulin heavy chain
  • antibody light chainImmunoglobulin light chain
KeywordsPROTEIN BINDING/IMMUNE SYSTEM / Beta propeller / PROTEIN BINDING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / kinase inhibitor activity / Wnt receptor activity / low-density lipoprotein particle receptor activity / toxin transmembrane transporter activity ...Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / kinase inhibitor activity / Wnt receptor activity / low-density lipoprotein particle receptor activity / toxin transmembrane transporter activity / Wnt-protein binding / cellular response to cholesterol / midbrain dopaminergic neuron differentiation / negative regulation of protein serine/threonine kinase activity / dopaminergic neuron differentiation / frizzled binding / neural crest cell differentiation / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of smooth muscle cell apoptotic process / canonical Wnt signaling pathway / coreceptor activity / positive regulation of cell cycle / Regulation of FZD by ubiquitination / TCF dependent signaling in response to WNT / protein localization to plasma membrane / cell-cell adhesion / response to peptide hormone / Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / cytoplasmic vesicle / early endosome membrane / membrane raft / signaling receptor binding / neuronal cell body / synapse / positive regulation of DNA-templated transcription / cell surface / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Low density lipoprotein receptor-related protein 5/6 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / TolB, C-terminal domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. ...Low density lipoprotein receptor-related protein 5/6 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / TolB, C-terminal domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / Laminin / Laminin / 6 Propeller / Neuraminidase / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, W. / Bourhis, E. / Tam, C. / Zhang, Y. / Rouge, L. / Wu, Y. / Franke, Y. / Cochran, A.G.
CitationJournal: Structure / Year: 2011
Title: Wnt antagonists bind through a short peptide to the first beta-propeller domain of LRP5/6.
Authors: Bourhis, E. / Wang, W. / Tam, C. / Hwang, J. / Zhang, Y. / Spittler, D. / Huang, O.W. / Gong, Y. / Estevez, A. / Zilberleyb, I. / Rouge, L. / Chiu, C. / Wu, Y. / Costa, M. / Hannoush, R.N. / ...Authors: Bourhis, E. / Wang, W. / Tam, C. / Hwang, J. / Zhang, Y. / Spittler, D. / Huang, O.W. / Gong, Y. / Estevez, A. / Zilberleyb, I. / Rouge, L. / Chiu, C. / Wu, Y. / Costa, M. / Hannoush, R.N. / Franke, Y. / Cochran, A.G.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2May 14, 2014Group: Refinement description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: antibody light chain
B: Low-density lipoprotein receptor-related protein 6
H: antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5224
Polymers88,4823
Non-polymers401
Water8,755486
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.037, 83.363, 62.844
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody antibody light chain / Immunoglobulin light chain


Mass: 25823.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Protein Low-density lipoprotein receptor-related protein 6 / LRP-6


Mass: 35422.859 Da / Num. of mol.: 1 / Fragment: UNP residues 20-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP6 / Production host: Escherichia coli (E. coli) / References: UniProt: O75581
#3: Antibody antibody heavy chain / Immunoglobulin heavy chain


Mass: 27235.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M NaCl, 0.1 M Tris pH 8, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979464 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979464 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 10 / Num. obs: 57170 / % possible obs: 91.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-1.97157.9
1.97-2.05178
2.05-2.14197.1
2.14-2.25197.4
2.25-2.39197.4
2.39-2.58197.6
2.58-2.84198.1
2.84-3.25198.4
3.25-4.09198.7
4.09-30197.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.071 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 2878 5.04 %5 percent
Rwork0.1739 ---
obs0.1758 57126 91.58 %-
all-62378 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.104 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.8893 Å20 Å24.3676 Å2
2--24.9869 Å20 Å2
3----9.0975 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5700 0 1 486 6187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085848
X-RAY DIFFRACTIONf_angle_d1.1867952
X-RAY DIFFRACTIONf_dihedral_angle_d15.2482077
X-RAY DIFFRACTIONf_chiral_restr0.086882
X-RAY DIFFRACTIONf_plane_restr0.0051021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9380.3368710.27831421X-RAY DIFFRACTION51
1.938-1.97150.27321010.23861689X-RAY DIFFRACTION61
1.9715-2.00730.2721170.22871912X-RAY DIFFRACTION68
2.0073-2.04590.28141070.21022262X-RAY DIFFRACTION80
2.0459-2.08760.29411420.22862717X-RAY DIFFRACTION96
2.0876-2.1330.22841480.19992700X-RAY DIFFRACTION97
2.133-2.18260.26771410.19882759X-RAY DIFFRACTION97
2.1826-2.23720.25621370.18952731X-RAY DIFFRACTION97
2.2372-2.29770.26041510.19382713X-RAY DIFFRACTION97
2.2977-2.36520.2481490.18182742X-RAY DIFFRACTION98
2.3652-2.44150.22971480.1792760X-RAY DIFFRACTION98
2.4415-2.52880.20891520.18282764X-RAY DIFFRACTION98
2.5288-2.62990.22531260.1782756X-RAY DIFFRACTION98
2.6299-2.74950.23731380.17932804X-RAY DIFFRACTION98
2.7495-2.89440.23881650.17442727X-RAY DIFFRACTION98
2.8944-3.07550.22071460.17282780X-RAY DIFFRACTION98
3.0755-3.31270.18991470.16482794X-RAY DIFFRACTION99
3.3127-3.64550.19841520.16222764X-RAY DIFFRACTION99
3.6455-4.17170.18361350.15392843X-RAY DIFFRACTION99
4.1717-5.25080.16761480.13972801X-RAY DIFFRACTION98
5.2508-29.07440.1841570.18122809X-RAY DIFFRACTION97
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)
10.21290.0365-0.11710.11330.06880.27260.01410.13990.04740.01460.0230.0165-0.02380.1498-00.23810.01990.00030.2952-0.00150.258232.8163-0.1543-1.7781
20.2405-0.0263-0.16730.19060.12580.1318-0.0477-0.01570.02430.0271-0.11640.00020.0498-0.091800.28930.0270.02680.3618-0.02550.301139.0835-22.9712-29.5177
30.4392-0.1089-0.03540.17890.09780.083-0.02280.1857-0.02230.01470.0285-0.0025-0.0195-0.0094-0.00010.22720.00750.00360.277-0.01810.238611.7527-8.0212-1.6913
40.08160.03430.08430.14420.18850.1557-0.0185-0.204-0.24320.0847-0.15340.05250.21940.02970.00010.36650.0220.0550.50240.06880.369529.6155-30.3204-18.4573
50.6960.198-0.36470.52950.02250.70680.0547-0.01790.02730.0123-0.03130.024-0.02570.079100.2085-0.0175-0.00790.16450.00360.20339.791415.035726.9572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 1:110 )L1 - 110
2X-RAY DIFFRACTION2( CHAIN L AND RESID 111:213 )L111 - 213
3X-RAY DIFFRACTION3( CHAIN H AND RESID 1:114 )H1 - 114
4X-RAY DIFFRACTION4( CHAIN H AND RESID 115:214 )H115 - 214
5X-RAY DIFFRACTION5( CHAIN B AND ( RESID 20:324 OR RESID 336:515 ) )B20 - 324
6X-RAY DIFFRACTION5( CHAIN B AND ( RESID 20:324 OR RESID 336:515 ) )B336 - 515

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