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- PDB-4dg6: Crystal structure of domains 1 and 2 of LRP6 -

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Basic information

Entry
Database: PDB / ID: 4dg6
TitleCrystal structure of domains 1 and 2 of LRP6
ComponentsLow-density lipoprotein receptor-related protein 6
KeywordsSIGNALING PROTEIN / 6-bladed beta propeller / sclerostin receptor / EGF / Wnt / MESD
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 / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / Wnt receptor 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 / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / Wnt receptor activity / cellular response to cholesterol / midbrain dopaminergic neuron differentiation / Wnt-protein binding / negative regulation of protein serine/threonine kinase activity / dopaminergic neuron differentiation / frizzled binding / Wnt signalosome / neural crest cell differentiation / 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 / Wnt signaling pathway / response to peptide hormone / positive regulation of DNA-binding transcription factor activity / cell-cell adhesion / early endosome membrane / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / chemical synaptic transmission / 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 / TolB, C-terminal domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD 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 / TolB, C-terminal domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD 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 / 6 Propeller / Neuraminidase / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Low-density lipoprotein receptor-related protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsCeska, T.A. / Doyle, C. / Slocombe, P.
CitationJournal: To be Published
Title: Characterization of the interaction of sclerostin with the LRP family of Wnt co-receptors
Authors: Holdsworth, G. / Slocombe, P. / Doyle, C. / Sweeney, B. / Veverka, V. / Le Rich, K. / Franklin, R.J. / Brookings, D. / Turner, J. / Kennedy, J. / Garlish, R. / Shi, J. / Newnham, L. / ...Authors: Holdsworth, G. / Slocombe, P. / Doyle, C. / Sweeney, B. / Veverka, V. / Le Rich, K. / Franklin, R.J. / Brookings, D. / Turner, J. / Kennedy, J. / Garlish, R. / Shi, J. / Newnham, L. / McMillan, D. / Muzylak, M. / Carr, M. / Henry, A.J. / Ceska, T. / Robinson, M.K.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
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_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low-density lipoprotein receptor-related protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0726
Polymers69,6091
Non-polymers1,4635
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.360, 109.360, 130.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Low-density lipoprotein receptor-related protein 6 / LRP-6


Mass: 69608.562 Da / Num. of mol.: 1 / Fragment: UNP residues 20-635
Source method: isolated from a genetically manipulated source
Details: Transient expression / Source: (gene. exp.) Homo sapiens (human) / Gene: LRP6 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O75581
#2: 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.: 3
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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 292 K / Method: hanging drop / pH: 5.9
Details: 20% PEG 8000, 20mM ammonium sulfate, pH 5.9, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.88→32.72 Å / Num. all: 21004 / Num. obs: 21004 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rsym value: 0.052 / Net I/σ(I): 25
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.88-2.957.50.7081.10.708199.9
2.95-3.037.50.5541.40.554199.2
3.03-3.127.40.4131.90.413199.5
3.12-3.227.50.2922.60.292199.9
3.22-3.327.40.2343.30.234199.3
3.32-3.447.40.1664.60.1661100
3.44-3.577.30.1196.50.119199.6
3.57-3.717.30.0878.70.087199.5
3.71-3.887.30.06112.20.061199.7
3.88-4.077.30.05313.90.053199.8
4.07-4.297.30.04217.30.0421100
4.29-4.557.30.03420.30.034199.9
4.55-4.867.10.03220.03199.6
4.86-5.257.10.02922.80.029199.8
5.25-5.757.20.03122.20.0311100
5.75-6.437.20.02923.10.0291100
6.43-7.437.10.02526.60.0251100
7.43-9.0970.02229.70.0221100
9.09-12.866.60.01736.90.0171100
12.86-32.725.40.01735.70.017191.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å32.09 Å
Translation3.5 Å32.09 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASER1.3.1phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→32.09 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.313 2009 9.8 %
Rwork0.257 --
obs0.257 20470 99.7 %
Displacement parametersBiso mean: 74.12 Å2
Baniso -1Baniso -2Baniso -3
1--11.907 Å2-16.741 Å20 Å2
2---11.907 Å20 Å2
3---23.813 Å2
Refinement stepCycle: LAST / Resolution: 2.9→32.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 94 13 5005
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.9891.5
X-RAY DIFFRACTIONc_mcangle_it1.7982
X-RAY DIFFRACTIONc_scbond_it0.9912
X-RAY DIFFRACTIONc_scangle_it1.6952.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:PROTEIN_REP.PARAMMSI_CNX_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2MSI_CNX_TOPPAR:CARBOHYDRATE.PARAMMSI_CNX_TOPPAR:CARBOHYDRATE.TOP
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:WATER_REP.PARAMMSI_CNX_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:ION.PARAMMSI_CNX_TOPPAR:ION.TOP

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