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- PDB-3sov: The structure of a beta propeller domain in complex with peptide S -

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Basic information

Entry
Database: PDB / ID: 3sov
TitleThe structure of a beta propeller domain in complex with peptide S
Components
  • Low-density lipoprotein receptor-related protein 6
  • Sclerostin
KeywordsProtein Binding/Antagonist / beta propeller / Protein Binding-Antagonist 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 / BMP binding / kinase inhibitor activity / toxin transmembrane transporter activity / low-density lipoprotein particle 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 / BMP binding / 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 / negative regulation of ossification / neural crest cell differentiation / Wnt signalosome / cellular response to parathyroid hormone stimulus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / molecular function inhibitor activity / negative regulation of Wnt signaling pathway / negative regulation of smooth muscle cell apoptotic process / negative regulation of BMP signaling pathway / localization / canonical Wnt signaling pathway / negative regulation of protein-containing complex assembly / BMP signaling pathway / coreceptor activity / positive regulation of cell cycle / response to mechanical stimulus / Regulation of FZD by ubiquitination / ossification / TCF dependent signaling in response to WNT / protein localization to plasma membrane / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / response to peptide hormone / positive regulation of DNA-binding transcription factor activity / cell-cell adhesion / heparin binding / early endosome membrane / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / carbohydrate binding / chemical synaptic transmission / DNA-binding transcription factor binding / membrane raft / signaling receptor binding / neuronal cell body / synapse / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Sclerostin/Sclerostin domain-containing protein 1 / Sclerostin (SOST) / Low density lipoprotein receptor-related protein 5/6 / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / 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 ...Sclerostin/Sclerostin domain-containing protein 1 / Sclerostin (SOST) / Low density lipoprotein receptor-related protein 5/6 / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / 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 / Cystine-knot cytokine / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Laminin / Coagulation Factor Xa inhibitory site / Laminin / 6 Propeller / Neuraminidase / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / Low-density lipoprotein receptor-related protein 6 / Sclerostin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsWang, W. / Bourhis, E. / 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 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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_ref_seq_dif.details
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
Z: Sclerostin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,82611
Polymers36,4512
Non-polymers1,3759
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint23 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.567, 47.090, 68.720
Angle α, β, γ (deg.)90.00, 97.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-930-

HOH

21A-931-

HOH

31A-932-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AZ

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


Mass: 35685.926 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75581
#2: Protein/peptide Sclerostin


Mass: 764.917 Da / Num. of mol.: 1 / Fragment: UNP residues 115-121 / Source method: obtained synthetically / Details: peptide S / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BQB4

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Sugars , 2 types, 6 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#4: Sugar
ChemComp-FUC / alpha-L-fucopyranose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 342 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M potassium thiocyanate and 30% (w/v) PEG MME 2000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.27→30 Å / Num. all: 91213 / Num. obs: 89480 / % possible obs: 98.1 % / Observed criterion σ(I): 2.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→26.773 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 16.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1797 4276 5.04 %
Rwork0.1528 --
obs0.1541 84804 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.483 Å2 / ksol: 0.474 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5381 Å2-0 Å23.7299 Å2
2---0.2615 Å2-0 Å2
3---0.4412 Å2
Refinement stepCycle: LAST / Resolution: 1.27→26.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 86 339 2896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162791
X-RAY DIFFRACTIONf_angle_d1.7853812
X-RAY DIFFRACTIONf_dihedral_angle_d14.9161038
X-RAY DIFFRACTIONf_chiral_restr0.115423
X-RAY DIFFRACTIONf_plane_restr0.01491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.28470.35681200.30682551X-RAY DIFFRACTION94
1.2847-1.29990.33341500.27422593X-RAY DIFFRACTION96
1.2999-1.31570.26951440.25252621X-RAY DIFFRACTION97
1.3157-1.33240.27261320.23222646X-RAY DIFFRACTION97
1.3324-1.34990.2461530.22032668X-RAY DIFFRACTION97
1.3499-1.36840.25071420.20112626X-RAY DIFFRACTION97
1.3684-1.38790.24951340.18962691X-RAY DIFFRACTION97
1.3879-1.40870.20421460.16812613X-RAY DIFFRACTION97
1.4087-1.43070.23161360.16532651X-RAY DIFFRACTION97
1.4307-1.45410.1941580.15812642X-RAY DIFFRACTION98
1.4541-1.47920.22391370.15342646X-RAY DIFFRACTION98
1.4792-1.50610.20491590.15412634X-RAY DIFFRACTION98
1.5061-1.53510.18571510.13792701X-RAY DIFFRACTION98
1.5351-1.56640.19171580.13162647X-RAY DIFFRACTION98
1.5664-1.60040.17561320.13432672X-RAY DIFFRACTION98
1.6004-1.63770.19191580.13482695X-RAY DIFFRACTION98
1.6377-1.67860.18761400.13292700X-RAY DIFFRACTION98
1.6786-1.7240.18191230.12772711X-RAY DIFFRACTION98
1.724-1.77470.18721600.12672667X-RAY DIFFRACTION99
1.7747-1.8320.17471290.12952710X-RAY DIFFRACTION99
1.832-1.89740.13171310.1212743X-RAY DIFFRACTION99
1.8974-1.97340.17571340.12392710X-RAY DIFFRACTION99
1.9734-2.06320.15411410.1292716X-RAY DIFFRACTION99
2.0632-2.17190.1521580.13122697X-RAY DIFFRACTION99
2.1719-2.30790.1581360.13192762X-RAY DIFFRACTION100
2.3079-2.4860.1611430.13822739X-RAY DIFFRACTION99
2.486-2.73590.15811210.14982786X-RAY DIFFRACTION100
2.7359-3.13130.17061520.15482766X-RAY DIFFRACTION100
3.1313-3.94310.17711430.15352766X-RAY DIFFRACTION100
3.9431-26.77920.18821550.18452758X-RAY DIFFRACTION97

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