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- PDB-5fww: Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4) -

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Basic information

Entry
Database: PDB / ID: 5fww
TitleWnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4)
Components
  • DICKKOPF-RELATED PROTEIN 1
  • KREMEN PROTEIN 1
  • LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6
KeywordsSIGNALING PROTEIN / WNT / CELL SURFACE / SIGNALLING / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of mesodermal cell fate specification / regulation of endodermal cell fate specification / positive regulation of Wnt signaling pathway, calcium modulating pathway / Wnt signaling pathway involved in somitogenesis / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / Signaling by LRP5 mutants / motor learning / regulation of dopaminergic neuron differentiation / Wnt-Frizzled-LRP5/6 complex ...negative regulation of mesodermal cell fate specification / regulation of endodermal cell fate specification / positive regulation of Wnt signaling pathway, calcium modulating pathway / Wnt signaling pathway involved in somitogenesis / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / Signaling by LRP5 mutants / motor learning / regulation of dopaminergic neuron differentiation / Wnt-Frizzled-LRP5/6 complex / negative regulation of cardiac muscle cell differentiation / endoderm formation / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / synapse pruning / neural crest formation / Signaling by RNF43 mutants / heart induction / negative regulation of axon regeneration / receptor antagonist activity / endocardial cushion development / regulation of receptor internalization / kinase inhibitor activity / toxin transmembrane transporter activity / Wnt receptor activity / co-receptor binding / low-density lipoprotein particle receptor activity / positive regulation of Wnt signaling pathway, planar cell polarity pathway / Wnt-protein binding / cell communication / cellular response to cholesterol / heart valve development / midbrain dopaminergic neuron differentiation / dopaminergic neuron differentiation / frizzled binding / negative regulation of presynapse assembly / Wnt signalosome / negative regulation of ossification / embryonic limb morphogenesis / limb development / regulation of canonical Wnt signaling pathway / Disassembly of the destruction complex and recruitment of AXIN to the membrane / neural crest cell differentiation / face morphogenesis / low-density lipoprotein particle receptor binding / negative regulation of SMAD protein signal transduction / negative regulation of Wnt signaling pathway / negative regulation of smooth muscle cell apoptotic process / mesoderm formation / protein serine/threonine kinase inhibitor activity / negative regulation of BMP signaling pathway / hair follicle development / canonical Wnt signaling pathway / response to retinoic acid / forebrain development / coreceptor activity / regulation of synaptic transmission, glutamatergic / regulation of neuron apoptotic process / positive regulation of cell cycle / negative regulation of protein binding / Regulation of FZD by ubiquitination / protein localization to plasma membrane / TCF dependent signaling in response to WNT / positive regulation of JNK cascade / growth factor activity / negative regulation of canonical Wnt signaling pathway / cell-cell adhesion / cell morphogenesis / response to peptide hormone / Wnt signaling pathway / endocytosis / transmembrane signaling receptor activity / nervous system development / negative regulation of neuron projection development / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / early endosome membrane / chemical synaptic transmission / learning or memory / membrane raft / signaling receptor binding / neuronal cell body / apoptotic process / synapse / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / : / Dickkopf, N-terminal cysteine-rich / Dickkopf-like protein / : / : / Dickkopf N-terminal cysteine-rich region / Dickkopf-related protein 1/2/4, C-terminal subdomain 2 / Dickkopf-related protein 1/2/4, C-terminal subdomain 1 / Kremen ...: / : / Dickkopf, N-terminal cysteine-rich / Dickkopf-like protein / : / : / Dickkopf N-terminal cysteine-rich region / Dickkopf-related protein 1/2/4, C-terminal subdomain 2 / Dickkopf-related protein 1/2/4, C-terminal subdomain 1 / Kremen / : / Lipase, subunit A / Lipase, subunit A / Low density lipoprotein receptor-related protein 5/6 / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / : / Plasminogen Kringle 4 / Plasminogen Kringle 4 / TolB, C-terminal domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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 / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 6 / Dickkopf-related protein 1 / Kremen protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.5 Å
AuthorsZebisch, M. / Jackson, V.A. / Jones, E.Y.
CitationJournal: Structure / Year: 2016
Title: Structure of the Dual-Mode Wnt Regulator Kremen1 and Insight Into Ternary Complex Formation with Lrp6 and Dickkopf
Authors: Zebisch, M. / Jackson, V.A. / Zhao, Y. / Jones, E.Y.
History
DepositionFeb 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: KREMEN PROTEIN 1
C: DICKKOPF-RELATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4704
Polymers112,4303
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.933, 100.080, 270.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6 / LRP-6


Mass: 70093.898 Da / Num. of mol.: 1 / Fragment: PE3PE4, RESIDUES 630-1246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: LRP6 / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: O75581
#2: Protein KREMEN PROTEIN 1 / DICKKOPF RECEPTOR / KRINGLE DOMAIN-CONTAINING TRANSMEMBRANE PROTEIN 1 / KRINGLE-CONTAINING PROTEIN ...DICKKOPF RECEPTOR / KRINGLE DOMAIN-CONTAINING TRANSMEMBRANE PROTEIN 1 / KRINGLE-CONTAINING PROTEIN MARKING THE EYE AND THE NOSE


Mass: 32728.531 Da / Num. of mol.: 1 / Fragment: ECD, RESIDUES 30-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: KREMEN1, KREMEN, KRM1 / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q96MU8
#3: Protein DICKKOPF-RELATED PROTEIN 1 / HDKK-1 / SK


Mass: 9607.076 Da / Num. of mol.: 1 / Fragment: CRD2, RESIDUES 182-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: DKK1, UNQ492/PRO1008 / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: O94907
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE
Crystal growpH: 7.5 / Details: 20 %W/V PEG3350 0.2 M NA/K-PHOSPHATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→67.68 Å / Num. obs: 8070 / % possible obs: 51.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Net I/σ(I): 4.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.5→135.36 Å / Cor.coef. Fo:Fc: 0.763 / Cor.coef. Fo:Fc free: 0.701 / Cross valid method: THROUGHOUT / ESU R Free: 1.576 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.35528 388 4.8 %RANDOM
Rwork0.32128 ---
obs0.32284 7644 52.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.615 Å2
Baniso -1Baniso -2Baniso -3
1--15.63 Å20 Å20 Å2
2--32.79 Å20 Å2
3----17.17 Å2
Refinement stepCycle: LAST / Resolution: 3.5→135.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7729 0 1 0 7730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197934
X-RAY DIFFRACTIONr_bond_other_d00.027294
X-RAY DIFFRACTIONr_angle_refined_deg0.9981.93810764
X-RAY DIFFRACTIONr_angle_other_deg3.79316754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0335970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87223.487390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.941151295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5331564
X-RAY DIFFRACTIONr_chiral_restr0.0610.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219085
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021947
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_it1.2855.863898
X-RAY DIFFRACTIONr_mcbond_other1.2845.863897
X-RAY DIFFRACTIONr_mcangle_it2.3168.7874862
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9815.9034036
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.505→3.595 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 2 -
Rwork0.433 34 -
obs--3.36 %

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