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- PDB-2kvb: Solution structure of CI-MPR domain 5 bound to N-acetylglucosamin... -

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Basic information

Entry
Database: PDB / ID: 2kvb
TitleSolution structure of CI-MPR domain 5 bound to N-acetylglucosaminyl 6-phosphomethylmannoside
ComponentsCation-independent mannose-6-phosphate receptor
KeywordsPROTEIN TRANSPORT / TRANSPORT / LYSOSOME / MANNOSE / RECEPTOR / SUGAR BINDING / GLYCOPROTEIN / MEMBRANE / PHOSPHOPROTEIN / TRANSMEMBRANE / Disulfide bond
Function / homology
Function and homology information


kringle domain binding / insulin-like growth factor binding / lysosomal transport / D-mannose binding / endocytic vesicle / phosphoprotein binding / trans-Golgi network / late endosome / signaling receptor activity / endosome membrane ...kringle domain binding / insulin-like growth factor binding / lysosomal transport / D-mannose binding / endocytic vesicle / phosphoprotein binding / trans-Golgi network / late endosome / signaling receptor activity / endosome membrane / Golgi membrane / Golgi apparatus / cell surface / 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
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Model detailslowest energy, model 1
AuthorsOlson, L.J. / Peterson, F.C. / Volkman, B.F. / Dahms, N.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for recognition of phosphodiester-containing lysosomal enzymes by the cation-independent mannose 6-phosphate receptor.
Authors: Olson, L.J. / Peterson, F.C. / Castonguay, A. / Bohnsack, R.N. / Kudo, M. / Gotschall, R.R. / Canfield, W.M. / Volkman, B.F. / Dahms, N.M.
History
DepositionMar 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2013Group: Refinement description
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 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 1.5Nov 20, 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: Cation-independent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)16,7591
Polymers16,7591
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Cation-independent mannose-6-phosphate receptor / CI Man-6-P receptor / CI-MPR / M6PR / Insulin-like growth factor 2 receptor / Insulin-like growth ...CI Man-6-P receptor / CI-MPR / M6PR / Insulin-like growth factor 2 receptor / Insulin-like growth factor II receptor / IGF-II receptor / 300 kDa mannose 6-phosphate receptor / MPR 300


Mass: 16759.344 Da / Num. of mol.: 1 / Fragment: CI-MPR_domain5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: IGF2R, M6P / Plasmid: pPICZ-alpha-A / Production host: Pichia pastoris (fungus) / References: UniProt: P08169
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

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Sample preparation

DetailsContents: 1.25 mM [U-100% 13C; U-100% 15N] CI-MPR domain5-1, 10 mM [U-2H] bis-tris-2, 150 mM sodium chloride-3, 8 mM N-acetylglucosaminyl 6-phosphomethylmannoside-4, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.25 mMCI-MPR domain5-1[U-100% 13C; U-100% 15N]1
10 mMbis-tris-2[U-2H]1
150 mMsodium chloride-31
8 mMN-acetylglucosaminyl 6-phosphomethylmannoside-41
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: AMBIENT / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin2.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 2325 NOE CONSTRAINTS (416 INTRA, 546 SEQUENTIAL, 271 MEDIUM, and 1092 LONG RANGE) AND 189 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. AUTHOR STATES THAT THE ...Details: STRUCTURES ARE BASED ON A TOTAL OF 2325 NOE CONSTRAINTS (416 INTRA, 546 SEQUENTIAL, 271 MEDIUM, and 1092 LONG RANGE) AND 189 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. AUTHOR STATES THAT THE DATA WAS COLLECTED IN THE PRESENCE OF BOTH RECEPTOR AND LIGAND N-ACETYLGLUCOSAMINYL 6-PHOSPHOMETHYLMANNOSIDE. HOWEVER THE LIGAND COORDINATES WERE NOT REFINED AND THEREFORE NOT DEPOSITED
NMR constraintsNOE constraints total: 2325 / NOE intraresidue total count: 416 / NOE long range total count: 1092 / NOE medium range total count: 271 / NOE sequential total count: 546 / Protein phi angle constraints total count: 95 / Protein psi angle constraints total count: 94
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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