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- PDB-2l21: chicken IGF2R domain 11 -

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Basic information

Entry
Database: PDB / ID: 2l21
Titlechicken IGF2R domain 11
ComponentsCation-independent mannose-6-phosphate receptor
KeywordsTRANSPORT PROTEIN / Genomic imprinting / Insulin-like growth factor 2 / mannose 6 phosphate receptor / protein evolution
Function / homology
Function and homology information


insulin-like growth factor binding / lysosomal transport / D-mannose binding / membrane => GO:0016020 / 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
Fibronectin type-II domain-containing protein / Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing, simulated annealing
Model detailslowest energy, model 1
AuthorsWilliams, C. / Hoppe, H. / Strickland, M. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Forbes, B. / Jones, E.Y. ...Williams, C. / Hoppe, H. / Strickland, M. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Forbes, B. / Jones, E.Y. / Rezgui, D.Z. / Crump, M.P. / Hassan, A.B.
CitationJournal: To be Published
Title: CD loop dependency of the IGF2: M6P/IGF2 receptor binding interaction predates imprinting
Authors: Williams, C. / Hoppe, H. / Rezgui, D. / Strickland, M. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Jones, E.Y. / Forbes, B. / Crump, M.P. / Hassan, A.B.
History
DepositionAug 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / 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 1.2Jun 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 1.3Nov 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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cation-independent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)17,2371
Polymers17,2371
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 energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cation-independent mannose-6-phosphate receptor


Mass: 17237.201 Da / Num. of mol.: 1 / Fragment: domain 11, residues 1485-1630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: igf2r / Plasmid: pET26a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q90681, UniProt: F1NVD2*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Domain 11 of Gallus gallus Cation-independent mannose-6-phosphate receptor
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D C(CO)NH
1723D CBCA(CO)NH
1823D HN(CO)CA
1923D H(CCO)NH
11023D (H)CCH-TOCSY
11123D 1H-15N NOESY
11223D 1H-13C NOESY
11312D 1H-15N HSQC
NMR detailsText: Some backbone datasets acquired using ASCOM with a reduced number of points in the nitrogen dimension

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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, 95% H2O/5% D2O95% H2O/5% D2O
25% D2O, 20 mM sodium phosphate, 0.1 mM EDTA, 100 uM sodium azide, 0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 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
mMprotein-5[U-98% 15N]0.5-11
5 %D2O-62
20 mMsodium phosphate-72
0.1 mMEDTA-82
100 uMsodium azide-92
mMprotein-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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
TALOSCornilescu, Delaglio and Baxdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
iCingr765Vuister, Doreleijers, Sousa da Silvarefinement
CcpNmr Analysis2.13Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, Lauechemical shift assignment
CcpNmr Analysis2.13Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, Lauedata analysis
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 paramaters
NMR constraintsNOE constraints total: 3375 / NOE intraresidue total count: 1079 / NOE long range total count: 1111 / Hydrogen bond constraints total count: 32
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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