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- PDB-1e6f: Human MIR-receptor, repeat 11 -

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Basic information

Entry
Database: PDB / ID: 1e6f
TitleHuman MIR-receptor, repeat 11
ComponentsCATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
KeywordsRECEPTOR / MIR-RECEPTOR / IGF-II RECEPTOR / TRANSPORT / GLYCOPROTEIN
Function / homology
Function and homology information


clathrin coat / Retrograde transport at the Trans-Golgi-Network / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / retinoic acid binding ...clathrin coat / Retrograde transport at the Trans-Golgi-Network / response to tetrachloromethane / insulin-like growth factor receptor activity / retromer complex binding / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / D-mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / secretory granule membrane / trans-Golgi network membrane / post-embryonic development / phosphoprotein binding / trans-Golgi network / clathrin-coated endocytic vesicle membrane / liver development / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome / endosome membrane / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / enzyme binding / cell surface / Golgi apparatus / signal transduction / extracellular exosome / identical protein binding / membrane / 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
Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.75 Å
AuthorsVon Buelow, R. / Rajashankar, K.R. / Dauter, M. / Dauter, Z. / Grimme, S. / Schmidt, B. / Von Figura, K. / Uson, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Locating the Anomalous Scatterer Substructures in Halide and Sulfur Phasing
Authors: Uson, I. / Schmidt, B. / Von Buelow, R. / Grimme, S. / Von Figura, K. / Dauter, M. / Rajashankar, K.R. / Dauter, Z. / Sheldrick, G.M.
History
DepositionAug 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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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
B: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)31,1292
Polymers31,1292
Non-polymers00
Water2,126118
1
A: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)15,5651
Polymers15,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)15,5651
Polymers15,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.500, 49.000, 120.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.02057, -0.99979, -0.00014), (-0.95456, -0.0196, -0.29736), (0.2973, 0.00625, -0.95476)
Vector: 7.67511, 20.07979, 21.65717)

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Components

#1: Protein CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR / MANNOSE-6-PHOSPHATE RECEPTOR / INSULIN-LIKE GROWTH-FACTOR II RECEPTOR / CI MAN-6-P RECEPTOR / CI- ...MANNOSE-6-PHOSPHATE RECEPTOR / INSULIN-LIKE GROWTH-FACTOR II RECEPTOR / CI MAN-6-P RECEPTOR / CI-MPR / 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR / MPR 300


Mass: 15564.672 Da / Num. of mol.: 2
Fragment: IGF-II-BINDING DOMAIN, REPEAT 11, RESIDUES 1508-1650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: FIBROBLAST / Cell line: BHK-21 / Cellular location: LYSOSOME / Organ: KIDNEY / Production host: CRICETINAE GEN. SP. (mammal) / References: UniProt: P11717
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES FROM THE GOLGI COMPLEX AND THE CELL SURFACE TO ...TRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES FROM THE GOLGI COMPLEX AND THE CELL SURFACE TO LYSOSOMES. LYSOSOMAL ENZYMES BEARING PHOSPHOMANNOSYL RESIDUES BIND SPECIFICALLY TO MANNOSE-6-PHOSPHATE RECEPTORS IN THE GOLGI APPARATUS AND THE RESULTING RECEPTOR-LIGAND COMPLEX IS TRANSPORTED TO AN ACIDIC PRELYOSOMAL COMPARTMENT WHERE THE LOW PH MEDIATES THE DISSOCIATION OF THE COMPLEX. THIS RECEPTOR ALSO BINDS INSULIN GROWTH FACTOR II.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.7
Details: PRECIPITANT: 0.2 M AMMONIUM ACETATE, 0.1 M CACODYLATE PH 5 28% PEG 4000. PROTEIN SOLUTION: 8 MG/ML IN 10 MM TRIS-HCL PH7.5, 150 MM N VAPOUR DIFFUSION, HANGING DROPS,1:1 RATIO.
Crystal
*PLUS
Density % sol: 35 %
Crystal grow
*PLUS
Temperature: 288 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
210 mMTris-HCl1drop
3150 mM1dropNaCl
428 %PEG40001drop
50.2 Mammonium acetate1drop
6100 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 / Details: BENT CRYSTALS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9057 Å / Relative weight: 1
ReflectionResolution: 1.753→8 Å / Num. obs: 29383 / % possible obs: 99.1 % / Redundancy: 15 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 40.8
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 9.9 / % possible all: 97.3
Reflection
*PLUS
Lowest resolution: 8 Å / Redundancy: 8.3 %
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.089

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
DMphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.75→8 Å / Num. parameters: 8499 / Num. restraintsaints: 10697 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: REFINED OCCUPANCY FOR ALTERNATIVE DISORDERED SITES
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 1431 5 %RANDOM
all0.2223 29383 --
obs0.2209 -94.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 22 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2050.5
Refinement stepCycle: LAST / Resolution: 1.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 0 118 2067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0.017
X-RAY DIFFRACTIONs_from_restr_planes0.0288
X-RAY DIFFRACTIONs_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.2209
Solvent computation
*PLUS
Displacement parameters
*PLUS

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