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- PDB-2l29: Complex structure of E4 mutant human IGF2R domain 11 bound to IGF-II -

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Basic information

Entry
Database: PDB / ID: 2l29
TitleComplex structure of E4 mutant human IGF2R domain 11 bound to IGF-II
Components
  • Insulin-like growth factor 2 receptor variant
  • Insulin-like growth factor II
KeywordsTRANSPORT PROTEIN / mannose 6 phosphate receptor / Insulin-like growth factor 2 / Genomic imprinting / ligand trap
Function / homology
Function and homology information


spongiotrophoblast cell proliferation / negative regulation of muscle cell differentiation / Retrograde transport at the Trans-Golgi-Network / positive regulation of skeletal muscle tissue growth / clathrin coat / embryonic placenta morphogenesis / retromer complex binding / regulation of muscle cell differentiation / insulin-like growth factor receptor activity / response to tetrachloromethane ...spongiotrophoblast cell proliferation / negative regulation of muscle cell differentiation / Retrograde transport at the Trans-Golgi-Network / positive regulation of skeletal muscle tissue growth / clathrin coat / embryonic placenta morphogenesis / retromer complex binding / regulation of muscle cell differentiation / insulin-like growth factor receptor activity / response to tetrachloromethane / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / IRS-related events triggered by IGF1R / genomic imprinting / positive regulation of organ growth / insulin-like growth factor II binding / exocrine pancreas development / trans-Golgi network transport vesicle / positive regulation by host of viral process / positive regulation of multicellular organism growth / retinoic acid binding / lysosomal transport / positive regulation of vascular endothelial cell proliferation / Golgi Associated Vesicle Biogenesis / transmembrane receptor protein tyrosine kinase activator activity / nuclear envelope lumen / positive regulation of activated T cell proliferation / D-mannose binding / positive regulation of cell division / endocytic vesicle / positive regulation of glycogen biosynthetic process / G-protein alpha-subunit binding / embryonic placenta development / animal organ regeneration / SHC-related events triggered by IGF1R / response to retinoic acid / positive regulation of insulin receptor signaling pathway / transport vesicle / striated muscle cell differentiation / insulin-like growth factor receptor binding / post-embryonic development / positive regulation of mitotic nuclear division / receptor-mediated endocytosis / protein serine/threonine kinase activator activity / liver development / insulin-like growth factor receptor signaling pathway / secretory granule membrane / platelet alpha granule lumen / trans-Golgi network membrane / animal organ morphogenesis / phosphoprotein binding / insulin receptor binding / growth factor activity / clathrin-coated endocytic vesicle membrane / trans-Golgi network / hormone activity / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / glucose metabolic process / late endosome / integrin binding / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / insulin receptor signaling pathway / Clathrin-mediated endocytosis / signaling receptor activity / spermatogenesis / in utero embryonic development / positive regulation of MAPK cascade / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / endosome / receptor ligand activity / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Insulin-like growth factor II E-peptide, C-terminal / Insulin-like growth factor II / Insulin-like growth factor II E-peptide / 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 / Insulin-like, subunit E / Insulin-like ...Insulin-like growth factor II E-peptide, C-terminal / Insulin-like growth factor II / Insulin-like growth factor II E-peptide / 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 / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor / 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 / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Kringle-like fold / Distorted Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Insulin-like growth factor II / Cation-independent mannose-6-phosphate receptor / Insulin-like growth factor 2 receptor variant
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 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Oct 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
B: Insulin-like growth factor II


Theoretical massNumber of molelcules
Total (without water)22,9192
Polymers22,9192
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) / Plasmid: pET26a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q59EZ3, UniProt: P11717*PLUS
#2: Protein Insulin-like growth factor II / IGF-II / Somatomedin-A / Insulin-like growth factor II Ala-25 Del / Preptin


Mass: 7484.472 Da / Num. of mol.: 1 / Fragment: residues 25-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2, PP1446 / Plasmid: PGEM-TEASY / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P01344
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of IGF-II in complex with the mutant form of human domain 11 from the Cation-independent mannose-6-phosphate receptor
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-13C NOESY
1213D 1H-15N NOESY
1313D 1H-15N NOESY
1423D 1H-13C NOESY
1532D 1H-15N HSQC
1633D 1H-15N NOESY
1712D 1H-15N HSQC
1812D 1H-13C HSQC
1913D HNCO
11013D CBCA(CO)NH
11113D C(CO)NH
11213D HNCA
11313D HN(CA)CB
11413D HN(CA)CB
11513D (H)CCH-TOCSY
11613D HN(CO)CA
11713D H(CCO)NH
11813D 1H-15N NOESY
11913D 1H-13C NOESY
12022D 1H-15N HSQC
12122D 1H-13C HSQC
12223D CBCA(CO)NH
12323D C(CO)NH
12423D HNCO
12523D HNCA
12623D HN(CA)CB
12723D HN(CO)CA
12823D H(CCO)NH
12923D (H)CCH-TOCSY
13023D 1H-15N NOESY
13123D 1H-13C NOESY
13212D f2 filter NOESY
13322D f2 filter NOESY
13412D f2 filter NOESY
13522D f2 filter NOESY
13612D CN filtered NOESY
13722D CN filtered NOESY
13812D CN filtered NOESY
13922D CN filtered NOESY
14012D CN filtered TOCSY
14122D CN filtered TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA, 95% H2O/5% D2O95% H2O/5% D2O
20.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA, 95% H2O/5% D2O95% H2O/5% D2O
30.5-1 mM [U-98% 15N; U-95% 2H] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-98% 13C; U-98% 15N]0.5-11
mMentity_2-21.-1.51
5 %D2O-31
100 uMsodium azide-41
5 mMsodium acetate-51
0.1 mMEDTA-61
mMentity_2-7[U-98% 13C; U-98% 15N]0.5-12
mMentity_1-81.-1.52
5 %D2O-92
100 uMsodium azide-102
5 mMsodium acetate-112
0.1 mMEDTA-122
mMentity_2-13[U-98% 15N; U-95% 2H]0.5-13
mMentity_1-141.-1.53
5 %D2O-153
100 uMsodium azide-163
5 mMsodium acetate-173
0.1 mMEDTA-183
Sample conditionsIonic strength: 0 / pH: 4.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian VNMRSVarianVNMRS6002
Varian UnityPlusVarianUNITYPLUS9003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
iCingr765Vuister, Doreleijers, Sousa da Silvarefinement
Analysis2.13CCPNchemical shift assignment
Analysis2.13CCPNdata analysis
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure 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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