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Yorodumi- PDB-5gje: Three-dimensional reconstruction of human LRP6 ectodomain complex... -
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-Basic information
Entry | Database: PDB / ID: 5gje | |||||||||
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Title | Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Wnt signaling / Wnt co-receptor / LRP6 / glycoprotein / antagonist / Dkk1 / conformational change | |||||||||
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 / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / negative regulation of presynapse assembly / Signaling by LRP5 mutants / Wnt signaling pathway involved in somitogenesis / regulation of dopaminergic neuron differentiation / motor learning ...negative regulation of mesodermal cell fate specification / regulation of endodermal cell fate specification / positive regulation of Wnt signaling pathway, calcium modulating pathway / negative regulation of Wnt-Frizzled-LRP5/6 complex assembly / positive regulation of midbrain dopaminergic neuron differentiation / negative regulation of presynapse assembly / Signaling by LRP5 mutants / Wnt signaling pathway involved in somitogenesis / regulation of dopaminergic neuron differentiation / motor learning / Wnt-Frizzled-LRP5/6 complex / negative regulation of cardiac muscle cell differentiation / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / endoderm formation / synapse pruning / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / endocardial cushion development / regulation of receptor internalization / heart induction / receptor antagonist activity / kinase inhibitor activity / Wnt receptor activity / low-density lipoprotein particle receptor activity / toxin transmembrane transporter activity / co-receptor binding / negative regulation of smooth muscle cell apoptotic process / Wnt-protein binding / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cellular response to cholesterol / midbrain dopaminergic neuron differentiation / negative regulation of protein serine/threonine kinase activity / dopaminergic neuron differentiation / heart valve development / frizzled binding / negative regulation of ossification / neural crest cell differentiation / Wnt signalosome / embryonic limb morphogenesis / face morphogenesis / Disassembly of the destruction complex and recruitment of AXIN to the membrane / low-density lipoprotein particle receptor binding / limb development / negative regulation of Wnt signaling pathway / negative regulation of SMAD protein signal transduction / mesoderm formation / negative regulation of BMP signaling pathway / hair follicle development / canonical Wnt signaling pathway / coreceptor activity / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / regulation of neuron apoptotic process / response to retinoic acid / forebrain development / regulation of synaptic transmission, glutamatergic / Regulation of FZD by ubiquitination / negative regulation of protein binding / TCF dependent signaling in response to WNT / protein localization to plasma membrane / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / growth factor activity / cell morphogenesis / cell-cell adhesion / response to peptide hormone / Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of neuron projection development / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / cytoplasmic vesicle / early endosome membrane / learning or memory / membrane raft / signaling receptor binding / neuronal cell body / synapse / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 21 Å | |||||||||
Authors | Matoba, K. / Mihara, E. / Tamura-Kawakami, K. / Hirai, H. / Thompson, S. / Iwasaki, K. / Takagi, J. | |||||||||
Citation | Journal: Cell Rep / Year: 2017 Title: Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1. Authors: Kyoko Matoba / Emiko Mihara / Keiko Tamura-Kawakami / Naoyuki Miyazaki / Shintaro Maeda / Hidenori Hirai / Samuel Thompson / Kenji Iwasaki / Junichi Takagi / Abstract: LDL-receptor-related protein 6 (LRP6) is a single-pass membrane glycoprotein with a large modular ectodomain and forms a higher order signaling platform upon binding Wnt ligands on the cell surface. ...LDL-receptor-related protein 6 (LRP6) is a single-pass membrane glycoprotein with a large modular ectodomain and forms a higher order signaling platform upon binding Wnt ligands on the cell surface. Although multiple crystal structures are available for fragments of the LRP6 ectodomain, we lack a consensus view on the overall molecular architecture of the full-length LRP6 and its dynamic aspects. Here, we used negative-stain electron microscopy to probe conformational states of the entire ectodomain of LRP6 in solution and found that the four-module ectodomain undergoes a large bending motion hinged at the junction between the second and the third modules. Importantly, the extent of inter-domain motion is modulated by evolutionarily conserved N-glycan chains proximal to the joint. We also found that the LRP6 ectodomain becomes highly compact upon complexation with the Wnt antagonist Dkk1, suggesting a potential role for the ectodomain conformational change in the regulation of receptor oligomerization and signaling. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5gje.cif.gz | 403.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gje.ent.gz | 329.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/5gje ftp://data.pdbj.org/pub/pdb/validation_reports/gj/5gje | HTTPS FTP |
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-Related structure data
Related structure data | 9501MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Low-density lipoprotein receptor-related protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 69034.883 Da / Num. of mol.: 1 / Fragment: UNP residues 20-630 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LRP6 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O75581 |
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#2: Protein | Mass: 69810.609 Da / Num. of mol.: 1 / Fragment: UNP residues 631-1246 / Mutation: V1062I 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 |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 9607.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DKK1, UNQ492/PRO1008 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O94907 |
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-Sugars , 3 types, 8 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | |
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-Non-polymers , 3 types, 16 molecules
#6: Chemical | #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.21 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.2 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO / Details: This sample was monodisperse. | ||||||||||||||||||||||||||||
EM staining | Type: NONE / Material: Uranyl acetate | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. |
-Electron microscopy imaging
Microscopy | Model: HITACHI H-9500SD |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 80000 X / Cs: 2.8 mm |
Specimen holder | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Image recording | Average exposure time: 2 sec. / Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) |
Image scans | Sampling size: 24 µm / Width: 2048 / Height: 2048 |
-Processing
EM software |
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Image processing | Details: The selected images were band-pass filtered. | ||||||||||||||||||||||||||||||||||||
CTF correction | Details: This was not done for RCT but for following single-particle reconstruction Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Details: 10974 tilt pairs for RCT | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 21 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 5390 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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