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Yorodumi- PDB-4cnc: Crystal structure of human 5T4 (Wnt-activated inhibitory factor 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cnc | |||||||||
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Title | Crystal structure of human 5T4 (Wnt-activated inhibitory factor 1, Trophoblast glycoprotein) | |||||||||
Components | TROPHOBLAST GLYCOPROTEIN | |||||||||
Keywords | CELL ADHESION / WAIF1 / TPBG / TROVAX / CANCER / SIGNALING / LEUCINE-RICH REPEATS / WNT/BETA-CATENIN SIGNALING PATHWAY | |||||||||
Function / homology | Function and homology information mesenchymal cell migration / dendrite arborization / olfactory learning / positive regulation of chemotaxis / synaptic transmission, GABAergic / positive regulation of synapse assembly / axon terminus / cell chemotaxis / protein localization to plasma membrane / negative regulation of canonical Wnt signaling pathway ...mesenchymal cell migration / dendrite arborization / olfactory learning / positive regulation of chemotaxis / synaptic transmission, GABAergic / positive regulation of synapse assembly / axon terminus / cell chemotaxis / protein localization to plasma membrane / negative regulation of canonical Wnt signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / negative regulation of cell population proliferation / dendrite / cell surface / endoplasmic reticulum / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | |||||||||
Authors | Zhao, Y. / Malinauskas, T. / Harlos, K. / Jones, E.Y. | |||||||||
Citation | Journal: Structure / Year: 2014 Title: Structural Insights Into the Inhibition of Wnt Signaling by Cancer Antigen 5T4/Wnt-Activated Inhibitory Factor 1. Authors: Zhao, Y. / Malinauskas, T. / Harlos, K. / Jones, E.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cnc.cif.gz | 232.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cnc.ent.gz | 188 KB | Display | PDB format |
PDBx/mmJSON format | 4cnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cnc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4cnc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4cnc_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 4cnc_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/4cnc ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cnc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9999, -0.0099, -0.0092), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32900.395 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 60-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EMBRYONIC KIDNEY / Organ: KIDNEY / Plasmid: PURD-5T4/WAIF1ECTO / Cell line (production host): HEK293S GNTI- / Production host: HOMO SAPIENS (human) / References: UniProt: Q13641 |
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-Sugars , 2 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 201 molecules
#4: Chemical | ChemComp-PEG / #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 33 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop Details: THE CRYSTALLIZATION SITTING DROP CONTAINED 100 NL OF CONCENTRATED 5T4/WAIF1 (5 MG/ML IN 20 MM TRIS-HCL, PH 7.5, 150 MM NACL) PLUS 100 NL OF 0.2 M (NH4)2SO4, 30 % W/V PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.06 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2013 Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→54.33 Å / Num. obs: 59830 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.77→1.82 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T4, CRYSTAL FORM WITH 1 MOLECULE IN THE ASYMMETRIC UNIT Resolution: 1.77→54.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.104 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.234 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→54.33 Å
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Refine LS restraints |
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