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Yorodumi- PDB-5z55: NMR Solution Structure of the Kringle domain of human receptor ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z55 | ||||||||||||||||||
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Title | NMR Solution Structure of the Kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (ROR1) | ||||||||||||||||||
Components | Inactive tyrosine-protein kinase transmembrane receptor ROR1 | ||||||||||||||||||
Keywords | ONCOPROTEIN / ROR1 / Kringle | ||||||||||||||||||
Function / homology | Function and homology information WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / axon terminus / stress fiber / transmembrane receptor protein tyrosine kinase activity / sensory perception of sound ...WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / axon terminus / stress fiber / transmembrane receptor protein tyrosine kinase activity / sensory perception of sound / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of neuron projection development / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / receptor complex / phosphorylation / cell surface / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||||||||||||||
Authors | Ma, X. / Hu, K.F. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Biomol NMR Assign / Year: 2018 Title: Backbone and side-chain chemical shift assignments of the kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (ROR1). Authors: Ma, X. / Zhang, Y. / Liu, B. / Yang, J. / Hu, K. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z55.cif.gz | 247.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z55.ent.gz | 210 KB | Display | PDB format |
PDBx/mmJSON format | 5z55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/5z55 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/5z55 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9562.522 Da / Num. of mol.: 1 / Fragment: Kringle domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ROR1, NTRKR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01973 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 0.8 mM 99%U-13C, U-15N ROR1Kr, 94% H2O/6% D2O Details: Kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (ROR1) Label: 13C_15N_ROR1Kr / Solvent system: 94% H2O/6% D2O |
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Sample | Conc.: 0.8 mM / Component: ROR1Kr / Isotopic labeling: 99%U-13C, U-15N |
Sample conditions | Details: buffer: 25 mM Tris, 150 mM NaCl, 6% D2O and 0.02% NaN3 (w/v) at pH 8.0 and 298 K Ionic strength: 150 mM / Label: conditions_1 / pH: 8.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 6 | |||||||||||||||||||||
NMR representative | Selection criteria: medoid | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 96 / Conformers submitted total number: 10 |