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- PDB-5air: Structural analysis of mouse GSK3beta fused with LRP6 peptide. -

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Basic information

Entry
Database: PDB / ID: 5air
TitleStructural analysis of mouse GSK3beta fused with LRP6 peptide.
ComponentsLow-density lipoprotein receptor-related protein 6,Glycogen synthase kinase-3 beta
KeywordsTRANSFERASE / LRP6 / GSK3 BETA
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / B-WICH complex positively regulates rRNA expression / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / re-entry into mitotic cell cycle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists ...Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / B-WICH complex positively regulates rRNA expression / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / re-entry into mitotic cell cycle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / neural crest formation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Signaling by RNF43 mutants / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of cardiac muscle cell differentiation / myotube differentiation / Degradation of beta-catenin by the destruction complex / kinase inhibitor activity / toxin transmembrane transporter activity / protein localization to microtubule / Wnt receptor activity / negative regulation of cardiac muscle hypertrophy / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / GLI3 is processed to GLI3R by the proteasome / positive regulation of stem cell differentiation / low-density lipoprotein particle receptor activity / negative regulation of TORC2 signaling / Wnt-protein binding / cellular response to cholesterol / autosome genomic imprinting / positive regulation of cilium assembly / beta-catenin destruction complex / meiosis I / tau-protein kinase / midbrain dopaminergic neuron differentiation / dopaminergic neuron differentiation / myoblast fusion / regulation of microtubule-based process / regulation of protein export from nucleus / frizzled binding / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cellular response to interleukin-3 / phosphorylation / Wnt signalosome / axon extension / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / meiotic spindle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / neural crest cell differentiation / negative regulation of calcineurin-NFAT signaling cascade / tau-protein kinase activity / negative regulation of epithelial to mesenchymal transition / cellular response to glucocorticoid stimulus / cellular response to hepatocyte growth factor stimulus / ER overload response / glycogen metabolic process / regulation of neuron projection development / dynein complex binding / fat cell differentiation / negative regulation of smooth muscle cell apoptotic process / epithelial to mesenchymal transition / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / protein serine/threonine kinase inhibitor activity / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / positive regulation of axon extension / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / coreceptor activity / extrinsic apoptotic signaling pathway / positive regulation of cell cycle / extrinsic apoptotic signaling pathway in absence of ligand / cytoskeleton organization / positive regulation of autophagy / positive regulation of substrate adhesion-dependent cell spreading / TCF dependent signaling in response to WNT / axonogenesis / protein export from nucleus / lipopolysaccharide-mediated signaling pathway / dendritic shaft / animal organ morphogenesis / positive regulation of protein export from nucleus / protein localization to plasma membrane / stem cell differentiation / regulation of cell growth / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of canonical Wnt signaling pathway / regulation of circadian rhythm / cell-cell adhesion / beta-catenin binding / response to peptide hormone / Wnt signaling pathway / circadian rhythm / endocytosis / neuron projection development / peptidyl-serine phosphorylation / p53 binding / kinase activity / insulin receptor signaling pathway
Similarity search - Function
Low density lipoprotein receptor-related protein 5/6 / : / Glycogen synthase kinase 3, catalytic 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 ...Low density lipoprotein receptor-related protein 5/6 / : / Glycogen synthase kinase 3, catalytic 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 / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Low-density lipoprotein receptor-related protein 6 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.53 Å
AuthorsKim, K.L.
CitationJournal: Biodesign / Year: 2015
Title: Structural Analysis of Mouse Gsk3 Beta Fused with Lrp6 Peptide
Authors: Kim, K.L. / Kim, J.S. / Cha, J.S. / Cho, H.S. / Ha, N.C.
History
DepositionFeb 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_residues / struct_biol / struct_ref / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity.src_method / _entity_name_com.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low-density lipoprotein receptor-related protein 6,Glycogen synthase kinase-3 beta
B: Low-density lipoprotein receptor-related protein 6,Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8494
Polymers95,6452
Non-polymers2042
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-1.7 kcal/mol
Surface area33550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.902, 85.883, 177.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Low-density lipoprotein receptor-related protein 6,Glycogen synthase kinase-3 beta / LRP-6 / GSK-3 beta / Serine/threonine-protein kinase GSK3B


Mass: 47822.422 Da / Num. of mol.: 2
Fragment: RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420
Source method: isolated from a genetically manipulated source
Details: ac-to-Bac baculovirus expression system,ac-to-Bac baculovirus expression system
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Gene: LRP6, Gsk3b / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O75581, UniProt: Q9WV60, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.3 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200 MM SODIUM MALONATE, 20 % (V/V) PEG 3350, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→177.5 Å / Num. obs: 42941 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.37

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.53→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.218 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25983 2105 5 %RANDOM
Rwork0.21213 ---
obs0.21451 40183 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.199 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--2.13 Å20 Å2
3----3.43 Å2
Refinement stepCycle: LAST / Resolution: 2.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 14 23 5724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195823
X-RAY DIFFRACTIONr_bond_other_d0.0050.025633
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.987912
X-RAY DIFFRACTIONr_angle_other_deg0.872312974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36723.125256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.76515988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4541546
X-RAY DIFFRACTIONr_chiral_restr0.0910.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021317
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8944.7432850
X-RAY DIFFRACTIONr_mcbond_other3.8954.7432849
X-RAY DIFFRACTIONr_mcangle_it6.4347.0873552
X-RAY DIFFRACTIONr_mcangle_other6.4337.0873553
X-RAY DIFFRACTIONr_scbond_it3.7055.1332973
X-RAY DIFFRACTIONr_scbond_other3.7045.1332974
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1267.4974361
X-RAY DIFFRACTIONr_long_range_B_refined11.29343.05923876
X-RAY DIFFRACTIONr_long_range_B_other11.29443.06123875
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.534→2.599 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 146 -
Rwork0.355 2629 -
obs--90.27 %

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