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- PDB-2l2a: Mutated Domain 11 of the Cytoplasmic region of the Cation-indepen... -

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Basic information

Entry
Database: PDB / ID: 2l2a
TitleMutated Domain 11 of the Cytoplasmic region of the Cation-independent mannose-6-phosphate receptor
ComponentsInsulin-like growth factor 2 receptor variant
KeywordsTRANSPORT PROTEIN / mannose 6 phosphate receptor / protein evolution / Insulin-like growth factor 2 / Genomic imprinting
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 / G-protein alpha-subunit binding / endocytic vesicle / 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 membrane / endosome / 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 / Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, simulated annealing
Model detailslowest energy, model 1
AuthorsWilliams, C. / Hoppe, H. / Rezgui, D. / Strickland, M. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Forbes, B. ...Williams, C. / Hoppe, H. / Rezgui, D. / Strickland, M. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Forbes, B. / Jones, E.Y. / Crump, M.P. / Hassan, A.B.
CitationJournal: 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
DepositionAug 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-like growth factor 2 receptor variant


Theoretical massNumber of molelcules
Total (without water)15,4351
Polymers15,4351
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Insulin-like growth factor 2 receptor variant


Mass: 15434.524 Da / Num. of mol.: 1 / Fragment: domain 11, residues 1431-1570 / Mutation: E1544K, K1545S, L1547V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: igf2r / Plasmid: pET26a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q59EZ3, UniProt: P11717*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: E4 IGF2R domain 11
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HN(CO)CA
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D (H)CCH-TOCSY
11313D H(CCO)NH

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Sample preparation

DetailsContents: 5% D2O, 10 mM [U-99% 2H] sodium acetate, 0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 100 uM EDTA, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
5 %D2O-11
10 mMsodium acetate-2[U-99% 2H]1
mMentity-3[U-98% 13C; U-98% 15N]0.5-11
100 uMEDTA-41
Sample conditionsIonic strength: 0 / pH: 4.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
Analysis2.13CCPNchemical shift assignment
Analysis2.13CCPNdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
iCingr765Vuister, Doreleijers, Sousa da Silvarefinement
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
RefinementMethod: simulated annealing, simulated annealing / Software ordinal: 1
Details: ARIA2.2 protocol. Cool_1 and cool_2 steps increased to 40K and cool_2, ARIA2.2 water refinement modified with RECOORD water refinement parameters
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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