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- PDB-2cnj: NMR studies on the interaction of Insulin-Growth Factor II (IGF-I... -

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Basic information

Entry
Database: PDB / ID: 2cnj
TitleNMR studies on the interaction of Insulin-Growth Factor II (IGF-II) with IGF2R domain 11
ComponentsCATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
KeywordsRECEPTOR / TRANSPORT / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE / IGF2R / CANCER / MEMBRANE / LYSOSOME / INSULIN-LIKE GROWTH FACTOR-II
Function / homology
Function and homology information


clathrin coat / Retrograde transport at the Trans-Golgi-Network / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / retinoic acid binding ...clathrin coat / Retrograde transport at the Trans-Golgi-Network / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / D-mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / secretory granule membrane / trans-Golgi network membrane / post-embryonic development / phosphoprotein binding / trans-Golgi network / clathrin-coated endocytic vesicle membrane / liver development / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome / endosome membrane / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / enzyme binding / cell surface / Golgi apparatus / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Fibronectin type II domain / Fibronectin type II domain superfamily ...Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / WATER REFINED IN CNS
AuthorsWilliams, C. / Prince, S. / Zaccheo, O. / Hassan, A.B. / Crosby, J. / Crump, M.
CitationJournal: Structure / Year: 2007
Title: Structural Insights Into the Interaction of Insulin-Like Growth Factor 2 with Igf2R Domain 11.
Authors: Williams, C. / Rezgui, D. / Prince, S.N. / Zaccheo, O.J. / Foulstone, E.J. / Forbes, B.E. / Norton, R.S. / Crosby, J. / Hassan, A.B. / Crump, M.P.
History
DepositionMay 22, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)16,6521
Polymers16,6521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LOWEST ENERGY, LEAST VIOLATION
Representative

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Components

#1: Protein CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR / IGF2R DOMAIN 11 / CI MAN-6-P RECEPTOR / CI-MPR / M6PR / INSULIN-LIKE GROWTH FACTOR 2 RECEPTOR / ...IGF2R DOMAIN 11 / CI MAN-6-P RECEPTOR / CI-MPR / M6PR / INSULIN-LIKE GROWTH FACTOR 2 RECEPTOR / INSULIN-LIKE GROWTH FACTOR II RECEPTOR / IGF-II RECEPTOR / M6P/IGF2 RECEPTOR / M6P/IGF2R / 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR / MPR 300 / MPR300 / CD222 ANTIGEN


Mass: 16651.848 Da / Num. of mol.: 1 / Fragment: DOMAIN 11, RESIDUES 1508-1650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11717
Compound detailsPROMOTES THE TRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
121TOCSY
131NOESY
141HNCA
151HN(CA)CB
161CBCA(CO)NH
171(H)CCH- TCOSY
181HNHA
191HNBA
1101HNCO
1111HN(CA)CO
1121HN(CO)CA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON UNLABELLED, 15N AND 13C, 15N-LABELED DOMAIN 11.

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Sample preparation

DetailsContents: 5% D2O/ 95% H2O
Sample conditionspH: 5.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
NMRDrawstructure solution
NMRPipestructure solution
CNSstructure solution
RefinementMethod: WATER REFINED IN CNS / Software ordinal: 1
Details: WATER REFINED USING RECORRD SCIPTS IN CNS. A.J.NEDERVEEN,J.F.DORELEIJERS,W.VRANKEN, Z.MILLER, C.A.SPRONK, S.B.NABUURS, P.GUNTERT, M.LIVNY, J.L.MARKLEY, M.NILGES, E.L.ULRICH, R.KAPTEIN AND A. ...Details: WATER REFINED USING RECORRD SCIPTS IN CNS. A.J.NEDERVEEN,J.F.DORELEIJERS,W.VRANKEN, Z.MILLER, C.A.SPRONK, S.B.NABUURS, P.GUNTERT, M.LIVNY, J.L.MARKLEY, M.NILGES, E.L.ULRICH, R.KAPTEIN AND A.M.BONVIN, PROTEINS. RECOORD: A RECALCULATED COORDINATES DATABASE OF 500+ PROTEINS FROM THE PDB USING RESTRAINTS FROM THE BIOMAGRESBANK. PROTEINS 59, 662-672.
NMR ensembleConformer selection criteria: LOWEST ENERGY, LEAST VIOLATION
Conformers calculated total number: 200 / Conformers submitted total number: 20

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