+Open data
-Basic information
Entry | Database: PDB / ID: 8tzr | ||||||||||||
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Title | Structure of human Wnt3a bound to WLS and CALR | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN | ||||||||||||
Function / homology | Function and homology information Wnt signaling pathway involved in forebrain neuroblast division / positive regulation of dermatome development / axis elongation involved in somitogenesis / calcium ion transmembrane transport via low voltage-gated calcium channel / positive regulation of collateral sprouting in absence of injury / positive regulation of mesodermal cell fate specification / paraxial mesodermal cell fate commitment / cell proliferation in midbrain / spinal cord association neuron differentiation / Formation of the posterior neural plate ...Wnt signaling pathway involved in forebrain neuroblast division / positive regulation of dermatome development / axis elongation involved in somitogenesis / calcium ion transmembrane transport via low voltage-gated calcium channel / positive regulation of collateral sprouting in absence of injury / positive regulation of mesodermal cell fate specification / paraxial mesodermal cell fate commitment / cell proliferation in midbrain / spinal cord association neuron differentiation / Formation of the posterior neural plate / Wnt protein secretion / Calnexin/calreticulin cycle / COP9 signalosome assembly / cytolytic granule / Wnt-Frizzled-LRP5/6 complex / positive regulation of Wnt protein secretion / positive regulation of cell-cell adhesion mediated by cadherin / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / synaptic vesicle recycling / Signaling by RNF43 mutants / positive regulation of dendritic cell chemotaxis / WNT ligand biogenesis and trafficking / positive regulation of cardiac muscle cell differentiation / cortical granule / Assembly of Viral Components at the Budding Site / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / cell proliferation in forebrain / negative regulation of retinoic acid receptor signaling pathway / negative regulation of axon extension involved in axon guidance / cellular response to electrical stimulus / endoplasmic reticulum quality control compartment / complement component C1q complex binding / nuclear receptor-mediated glucocorticoid signaling pathway / secondary palate development / regulation of meiotic nuclear division / Specification of the neural plate border / cementum mineralization / response to glycoside / sequestering of calcium ion / somatic stem cell division / non-canonical Wnt signaling pathway / co-receptor binding / sarcoplasmic reticulum lumen / cardiac muscle cell fate commitment / protein folding in endoplasmic reticulum / presynapse assembly / hormone binding / hindbrain development / positive regulation of skeletal muscle tissue development / Wnt-protein binding / negative regulation of dopaminergic neuron differentiation / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / midbrain dopaminergic neuron differentiation / dorsal/ventral neural tube patterning / regulation of postsynapse to nucleus signaling pathway / cardiac muscle cell differentiation / molecular sequestering activity / exocrine pancreas development / mammary gland development / post-anal tail morphogenesis / frizzled binding / positive regulation of neural precursor cell proliferation / positive regulation of hepatocyte proliferation / Class B/2 (Secretin family receptors) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / myoblast differentiation / anterior/posterior axis specification / protein maturation by protein folding / Scavenging by Class F Receptors / Scavenging by Class A Receptors / cortical actin cytoskeleton organization / inner ear morphogenesis / midbrain development / nuclear androgen receptor binding / organelle membrane / cell fate commitment / cellular response to lithium ion / regulation of synapse organization / response to testosterone / negative regulation of fat cell differentiation / B cell proliferation / fat cell differentiation / heart looping / Formation of paraxial mesoderm / skeletal muscle cell differentiation / positive regulation of receptor internalization / hemopoiesis / mesoderm formation / regulation of presynapse assembly / protein localization to nucleus / positive regulation of Wnt signaling pathway / negative regulation of neuron differentiation / Transcriptional and post-translational regulation of MITF-M expression and activity / smooth endoplasmic reticulum / canonical Wnt signaling pathway / endomembrane system / regulation of microtubule cytoskeleton organization / positive regulation of cell cycle Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Qi, X. / Hu, Q. / Li, X. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Structure of human Wnt3a bound to WLS and CALR Authors: Qi, X. / Hu, Q. / Li, X. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tzr.cif.gz | 213.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tzr.ent.gz | 163.9 KB | Display | PDB format |
PDBx/mmJSON format | 8tzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/8tzr ftp://data.pdbj.org/pub/pdb/validation_reports/tz/8tzr | HTTPS FTP |
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-Related structure data
Related structure data | 41767MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 39421.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WNT3A / Production host: Homo sapiens (human) / References: UniProt: P56704 |
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#2: Protein | Mass: 62317.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WLS / Production host: Homo sapiens (human) / References: UniProt: Q5T9L3 |
#3: Protein | Mass: 48198.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27797 |
-Sugars , 1 types, 1 molecules
#4: Polysaccharide | alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 2 molecules
#5: Chemical | ChemComp-PAM / |
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#6: Chemical | ChemComp-POV / ( |
-Details
Has ligand of interest | Y |
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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 | Name: Wnt3a-WLS-CALR Complex / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113802 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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