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- PDB-2lla: NMR solution structure ensemble of domain 11 of the echidna M6P/I... -

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Basic information

Entry
Database: PDB / ID: 2lla
TitleNMR solution structure ensemble of domain 11 of the echidna M6P/IGF2R receptor
ComponentsMannose-6-phosphate/insulin-like growth factor II receptor
KeywordsTRANSPORT PROTEIN / monotreme / mannose-6-phosphate / IGF-II / domain 11
Function / homology
Function and homology information


lysosomal transport / D-mannose binding / trans-Golgi network / signaling receptor activity / endosome membrane / Golgi 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 speciesTachyglossus aculeatus (Australian echidna)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsStrickland, M. / Crump, M.P. / Williams, C. / Rezgui, D. / Ellis, R.Z. / Hoppe, H. / Frago, S. / Prince, S.N. / Zaccheo, O.J. / Forbes, B.E. ...Strickland, M. / Crump, M.P. / Williams, C. / Rezgui, D. / Ellis, R.Z. / Hoppe, H. / Frago, S. / Prince, S.N. / Zaccheo, O.J. / Forbes, B.E. / Jones, E. / Hassan, A.Z. / Wattana-Amorn, P.
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
DepositionNov 5, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Mannose-6-phosphate/insulin-like growth factor II receptor


Theoretical massNumber of molelcules
Total (without water)15,2981
Polymers15,2981
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 / 100STRUCTURES WITH THE LOWEST ENER
RepresentativeModel #1lowest energy

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Components

#1: Protein Mannose-6-phosphate/insulin-like growth factor II receptor


Mass: 15298.317 Da / Num. of mol.: 1 / Fragment: Domain 11 residues 1490-1628
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tachyglossus aculeatus (Australian echidna)
Gene: igf2r, m6p/igf2r / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95LC7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Echidna (Tachyglossus aculeatus) domain 11 of the mannose-6-phosphate/insulin-like growth factor 2 receptor (M6P/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 HN(CA)CB
1713D H(CCO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D HNCA
NMR detailsText: The structure was determined using a combination of NOE restraints, dihedral restraints predicted from TALOS and hydrogen bond restraints initially predicted from the homologous human domain 11 ...Text: The structure was determined using a combination of NOE restraints, dihedral restraints predicted from TALOS and hydrogen bond restraints initially predicted from the homologous human domain 11 IGF2R structure (2CNJ)

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Sample preparation

DetailsContents: 100 uM sodium azide, 10 mM sodium phosphate, 1 mM EDTA, 7 % D2O, 93 % H2O, 0.5 mM [U-95% 13C; U-95% 15N] M6P/IGF2_receptor, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uMsodium azide-11
10 mMsodium phosphate-21
1 mMEDTA-31
7 %D2O-41
93 %H2O-51
0.5 mMM6P/IGF2_receptor-6[U-95% 13C; U-95% 15N]1
Sample conditionsIonic strength: 0.01 / pH: 5.5 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian VNMRS600VarianVNMRS6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
ProcheckNMRLaskowski and MacArthurrefinement
VnmrJ2.2cVariancollection
Analysis2.1CCPNchemical shift assignment
Analysis2.1CCPNrefinement
Analysis2.1CCPNpeak picking
CS23D1Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G.data analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: RECOORD water refinement
NMR constraintsNOE constraints total: 2766 / NOE intraresidue total count: 1187 / NOE long range total count: 584 / Hydrogen bond constraints total count: 100 / Protein phi angle constraints total count: 75 / Protein psi angle constraints total count: 75
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LOWEST ENER
Conformers calculated total number: 100 / Conformers submitted total number: 20

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