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- PDB-3k41: Crystal structure of sCD-MPR mutant E19Q/K137M bound to Man-6-P -

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Basic information

Entry
Database: PDB / ID: 3k41
TitleCrystal structure of sCD-MPR mutant E19Q/K137M bound to Man-6-P
ComponentsCation-dependent mannose-6-phosphate receptor
KeywordsProtein transport / sugar binding protein / transport / lysosome / mannose / receptor / sugar binding / Glycoprotein / Membrane / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / Glycosphingolipid catabolism / Lysosome Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / protein targeting to lysosome / Clathrin-mediated endocytosis / lysosomal transport / trans-Golgi network / endosome / lysosomal membrane ...Retrograde transport at the Trans-Golgi-Network / Glycosphingolipid catabolism / Lysosome Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / protein targeting to lysosome / Clathrin-mediated endocytosis / lysosomal transport / trans-Golgi network / endosome / lysosomal membrane / protein domain specific binding / Golgi apparatus
Similarity search - Function
Cation-dependent mannose-6-phosphate receptor / Mannose-6-phosphate receptor / Mannose-6-phosphate receptor / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-mannopyranose / Cation-dependent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOlson, L.J. / Sun, G. / Bohnsack, R.N. / Peterson, F.C. / Dahms, N.M. / Kim, J.J.P.
CitationJournal: Biochemistry / Year: 2010
Title: Intermonomer interactions are essential for lysosomal enzyme binding by the cation-dependent mannose 6-phosphate receptor.
Authors: Olson, L.J. / Sun, G. / Bohnsack, R.N. / Peterson, F.C. / Dahms, N.M. / Kim, J.J.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cation-dependent mannose-6-phosphate receptor
B: Cation-dependent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2406
Polymers36,5472
Non-polymers1,6934
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint8 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.234, 77.112, 79.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cation-dependent mannose-6-phosphate receptor / / CD Man-6-P receptor / CD-MPR / 46 kDa mannose 6-phosphate receptor / MPR 46


Mass: 18273.494 Da / Num. of mol.: 2 / Fragment: UNP residues 29-182 / Mutation: E19Q, K137M, N31Q, N57Q, N68Q, N87Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: M6PR / Plasmid: pGAP / Production host: Pichia Pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P11456
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-M6D / 6-O-phosphono-beta-D-mannopyranose / beta-D-mannose-6-phosphate / 6-O-phosphono-beta-D-mannose / 6-O-phosphono-D-mannose / 6-O-phosphono-mannose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
b-D-Manp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, pH 6.5;25% PEG 2000MME; 0.2M ammonium acetate; 0.025M OBG, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26594 / % possible obs: 99.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.126 / Χ2: 5.316 / Net I/σ(I): 13
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.534 / Num. unique all: 2607 / Χ2: 2.074 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M6P

1m6p


Resolution: 1.9→38.56 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.255 2526 9.5 %
Rwork0.216 --
obs-25567 96.2 %
Solvent computationBsol: 50.155 Å2
Displacement parametersBiso max: 60.58 Å2 / Biso mean: 27.305 Å2 / Biso min: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1--1.394 Å20 Å20 Å2
2---0.784 Å20 Å2
3---2.178 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 110 161 2611
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3871.5
X-RAY DIFFRACTIONc_scbond_it2.1442
X-RAY DIFFRACTIONc_mcangle_it2.1532
X-RAY DIFFRACTIONc_scangle_it3.1422.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION4m6p.par
X-RAY DIFFRACTION5gol.par

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