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- PDB-2l2g: Solution structure of Opossum Domain 11 -

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Basic information

Entry
Database: PDB / ID: 2l2g
TitleSolution structure of Opossum Domain 11
ComponentsIGF2R DOMAIN 11
KeywordsSIGNALING PROTEIN / Insulin-like growth factor 2 / mannose 6 phosphate receptor / Genomic imprinting / protein evolution
Function / homology
Function and homology information


retromer complex binding / insulin-like growth factor binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / lysosomal transport / nuclear envelope lumen / D-mannose binding / endocytic vesicle / phosphoprotein binding / trans-Golgi network ...retromer complex binding / insulin-like growth factor binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / lysosomal transport / nuclear envelope lumen / D-mannose binding / endocytic vesicle / phosphoprotein binding / trans-Golgi network / late endosome / signaling receptor activity / early endosome / endosome membrane / Golgi membrane / cell surface / identical protein binding / 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
Insulin like growth factor 2 receptor
Similarity search - Component
Biological speciesMonodelphis domestica (gray short-tailed opossum)
MethodSOLUTION NMR / simulated annealing, simulated annealing
Model detailslowest energy, model 1
AuthorsWilliams, C. / Hoppe, H. / Rezgui, D. / Rezgui, M. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Forbes, B. ...Williams, C. / Hoppe, H. / Rezgui, D. / Rezgui, M. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Forbes, B. / Jones, E.Y. / Crump, M.P. / Bassim, A.H.
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 18, 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 25, 2015Group: Structure summary
Revision 1.3Nov 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGF2R DOMAIN 11


Theoretical massNumber of molelcules
Total (without water)16,6561
Polymers16,6561
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 IGF2R DOMAIN 11


Mass: 16655.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monodelphis domestica (gray short-tailed opossum)
Plasmid: pET26a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: F6SWY2*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Domain 11 of the IGF2R from Monodelphis domestica (Gray Short-tailed Opossum)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1322D 1H-13C HSQC
1423D CBCA(CO)NH
1523D C(CO)NH
1623D HNCO
1723D HNCA
1823D HN(CA)CB
1923D HN(CO)CA
11023D HNHA
11123D 1H-15N NOESY
11213D 1H-15N TOCSY
11323D (H)CCH-TOCSY
11423D 1H-13C NOESY
11513D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
15 % D2O, 20 mM sodium acetate, 0.1 mM EDTA, 100 uM sodium azide, 0.5-1 mM [U-98% 15N] IGF2R DOMAIN 11, 95% H2O/5% D2O95% H2O/5% D2O
25 mM D2O, 20 mM sodium acetate, 0.1 mM EDTA, 100 uM sodium azide, 0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R DOMAIN 11, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
5 %D2O-11
20 mMsodium acetate-21
0.1 mMEDTA-31
100 uMsodium azide-41
mMentity-5[U-98% 15N]0.5-11
5 mMD2O-62
20 mMsodium acetate-72
0.1 mMEDTA-82
100 uMsodium azide-92
mMentity-10[U-98% 13C; U-98% 15N]0.5-12
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 298 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
NameVersionDeveloperClassification
VnmrJVariancollection
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CcpNMR2.13CCPNchemical shift assignment
CcpNMR2.13CCPNdata analysis
CcpNMR2.13CCPNpeak picking
iCingr765Vuister, Doreleijers, Sousa da Silvarefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing, simulated annealing / Software ordinal: 1
Details: ARIA1.2 protocol. Cool_1 and cool_2 steps increased to 40K and cool_2, ARIA1.2 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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