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- PDB-2m68: NMR solution structure ensemble of 3-4D mutant domain 11 IGF2R in... -

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Basic information

Entry
Database: PDB / ID: 2m68
TitleNMR solution structure ensemble of 3-4D mutant domain 11 IGF2R in complex with IGF2 (domain 11 structure only)
ComponentsInsulin-like growth factor 2 receptor variant
KeywordsANTITUMOR PROTEIN / antitumor / directed evolution / high affinity
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / insulin-like growth factor receptor activity / response to tetrachloromethane / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / insulin-like growth factor receptor activity / response to tetrachloromethane / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host 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 / post-embryonic development / receptor-mediated endocytosis / liver development / secretory granule membrane / trans-Golgi network membrane / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / signaling receptor activity / 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 / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Fibronectin type II domain / Fibronectin type II domain superfamily ...Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / 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 / Insulin-like growth factor 2 receptor variant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsfewest violations, model1
AuthorsStrickland, M. / Williams, C. / Richards, E. / Minnall, L. / Crump, M.P. / Frago, S. / Hughes, J. / Garner, L. / Hoppe, H. / Rezgui, D. ...Strickland, M. / Williams, C. / Richards, E. / Minnall, L. / Crump, M.P. / Frago, S. / Hughes, J. / Garner, L. / Hoppe, H. / Rezgui, D. / Zaccheo, O.J. / Prince, S.N. / Hassan, A.B. / Whittaker, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Functional evolution of IGF2:IGF2R domain 11 binding generates novel structural interactions and a specific IGF2 antagonist.
Authors: Frago, S. / Nicholls, R.D. / Strickland, M. / Hughes, J. / Williams, C. / Garner, L. / Surakhy, M. / Maclean, R. / Rezgui, D. / Prince, S.N. / Zaccheo, O.J. / Ebner, D. / Sanegre, S. / Yu, S. ...Authors: Frago, S. / Nicholls, R.D. / Strickland, M. / Hughes, J. / Williams, C. / Garner, L. / Surakhy, M. / Maclean, R. / Rezgui, D. / Prince, S.N. / Zaccheo, O.J. / Ebner, D. / Sanegre, S. / Yu, S. / Buffa, F.M. / Crump, M.P. / Hassan, A.B.
History
DepositionMar 27, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jun 1, 2016Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 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
Item: _database_2.pdbx_DOI

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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)15,4341
Polymers15,4341
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 least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 15433.587 Da / Num. of mol.: 1 / Fragment: Domain 11 / Mutation: Q1571L ,S1466A, G1467K, K1468G, G1469W, L1470G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Domain 11 IGF2R / Production host: Escherichia coli (E. coli) / References: UniProt: Q59EZ3, UniProt: P11717*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Ensemble of 20 structures of the 3-4D mutant of domain 11 IGF2R in complex with IGF2. The structure concerns the domain 11 portion only. The mutant hosts 5 mutations in the AB loop in ...Details: Ensemble of 20 structures of the 3-4D mutant of domain 11 IGF2R in complex with IGF2. The structure concerns the domain 11 portion only. The mutant hosts 5 mutations in the AB loop in comparison to human domain 11 IGF2R.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
11213D 1H-13C NOESY aliphatic
2132Heteronuclear NOE ratio
2142Heteronuclear NOE ratio
2152T1 experiments
2162T1 experiments
2172T2 experiments
2182T2 experiments

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Sample preparation

Details
Solution-IDContentsSolvent system
1STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.93% H2O/7% D2O
2DYNAMICS STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.93% H2O/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.00541 atm310.15 K
20.00541 atm298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS6001
Varian VNMRSVarianVNMRS9002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesprocessing
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
CINGiCingDoreleijersrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
relax1.3.9Palmerdata analysis
relax1.3.9Palmerprocessing
Sparky2.6Goddarddata analysis
VnmrJ0.4Variancollection
CCPN_Analysis2.1CCPNchemical shift assignment
CCPN_Analysis2.1CCPNdata analysis
CCPN_Analysis2.1CCPNpeak picking
TALOSTALOS+Cornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3176 / NOE intraresidue total count: 1242 / NOE long range total count: 776 / Hydrogen bond constraints total count: 52
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.1 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.0066 Å / Distance rms dev error: 0.0003 Å

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