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Yorodumi- PDB-2lla: NMR solution structure ensemble of domain 11 of the echidna M6P/I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lla | ||||||
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Title | NMR solution structure ensemble of domain 11 of the echidna M6P/IGF2R receptor | ||||||
Components | Mannose-6-phosphate/insulin-like growth factor II receptor | ||||||
Keywords | TRANSPORT PROTEIN / monotreme / mannose-6-phosphate / IGF-II / domain 11 | ||||||
Function / homology | Function and homology information insulin-like growth factor binding / lysosomal transport / D-mannose binding / signaling receptor activity / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Tachyglossus aculeatus (Australian echidna) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Strickland, M. / Crump, M.P. / Williams, C. / Rezgui, D. / Ellis, R.Z. / Hoppe, H. / Frago, S. / Prince, S.N. / Zaccheo, O.J. / Forbes, B.E. ...Strickland, M. / Crump, M.P. / Williams, C. / Rezgui, D. / Ellis, R.Z. / Hoppe, H. / Frago, S. / Prince, S.N. / Zaccheo, O.J. / Forbes, B.E. / Jones, E. / Hassan, A.Z. / Wattana-Amorn, P. | ||||||
Citation | Journal: Science / Year: 2012 Title: An exon splice enhancer primes IGF2:IGF2R binding site structure and function evolution. Authors: Williams, C. / Hoppe, H.J. / Rezgui, D. / Strickland, M. / Forbes, B.E. / Grutzner, F. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Nolan, C.M. / Mungall, A. ...Authors: Williams, C. / Hoppe, H.J. / Rezgui, D. / Strickland, M. / Forbes, B.E. / Grutzner, F. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Nolan, C.M. / Mungall, A.J. / Jones, E.Y. / Crump, M.P. / Hassan, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lla.cif.gz | 814.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lla.ent.gz | 705.8 KB | Display | PDB format |
PDBx/mmJSON format | 2lla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/2lla ftp://data.pdbj.org/pub/pdb/validation_reports/ll/2lla | HTTPS FTP |
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-Related structure data
Related structure data | 2l29C 2l2aC 2l2gC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15298.317 Da / Num. of mol.: 1 / Fragment: Domain 11 residues 1490-1628 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tachyglossus aculeatus (Australian echidna) Gene: igf2r, m6p/igf2r / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95LC7 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Echidna (Tachyglossus aculeatus) domain 11 of the mannose-6-phosphate/insulin-like growth factor 2 receptor (M6P/IGF2R). | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using a combination of NOE restraints, dihedral restraints predicted from TALOS and hydrogen bond restraints initially predicted from the homologous human domain 11 ...Text: The structure was determined using a combination of NOE restraints, dihedral restraints predicted from TALOS and hydrogen bond restraints initially predicted from the homologous human domain 11 IGF2R structure (2CNJ) |
-Sample preparation
Details | Contents: 100 uM sodium azide, 10 mM sodium phosphate, 1 mM EDTA, 7 % D2O, 93 % H2O, 0.5 mM [U-95% 13C; U-95% 15N] M6P/IGF2_receptor, 93% H2O/7% D2O Solvent system: 93% H2O/7% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.01 / pH: 5.50 / Pressure: ambient / Temperature: 298.15 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: RECOORD water refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2766 / NOE intraresidue total count: 1187 / NOE long range total count: 584 / Hydrogen bond constraints total count: 100 / Protein phi angle constraints total count: 75 / Protein psi angle constraints total count: 75 | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH THE LOWEST ENER Conformers calculated total number: 100 / Conformers submitted total number: 20 |