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- PDB-2kva: SOLUTION STRUCTURE OF CI-MPR ligand-free domain 5 -

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Basic information

Entry
Database: PDB / ID: 2kva
TitleSOLUTION STRUCTURE OF CI-MPR ligand-free domain 5
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-independent mannose-6-phosphate receptor repeat / 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 / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Fibronectin type II domain / Fibronectin type II domain superfamily ...Cation-independent mannose-6-phosphate receptor repeat / 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 / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / 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 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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

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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
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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) / Strain (production host): X-33 / References: UniProt: P08169

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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 mM [U-100% 13C; U-100% 15N] CI-MPR domain5-1, 10 mM [U-2H] bis-tris-2, 150 mM sodium chloride-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCI-MPR domain5-1[U-100% 13C; U-100% 15N]1
10 mMbis-tris-2[U-2H]1
150 mMsodium chloride-31
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: AMBIENT atm / 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 2050 NOE CONSTRAINTS (439 INTRA, 434 SEQUENTIAL, 182 MEDIUM, and 995 LONG RANGE) AND 165 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 2050 / NOE intraresidue total count: 439 / NOE long range total count: 995 / NOE medium range total count: 182 / NOE sequential total count: 434 / Protein phi angle constraints total count: 81 / Protein psi angle constraints total count: 84
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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