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- PDB-2rl8: Crystal Structure cation-dependent mannose 6-phosphate receptor a... -

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Basic information

Entry
Database: PDB / ID: 2rl8
TitleCrystal Structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to M6P
ComponentsCation-dependent mannose-6-phosphate receptor
KeywordsProtein transport / sugar binding protein / P-type lectin / receptor / mannose 6-phosphate / lectin / Glycoprotein / Lysosome / Membrane / Transmembrane / Transport
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 / protein domain specific binding ...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 / protein domain specific binding / lysosomal membrane / 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 / SYNCHROTRON / Resolution: 1.45 Å
AuthorsOlson, L.J. / Hindsgaul, O. / Kim, J.-J.P. / Dahms, N.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Insights into the Mechanism of pH-dependent Ligand Binding and Release by the Cation-dependent Mannose 6-Phosphate Receptor.
Authors: Olson, L.J. / Hindsgaul, O. / Dahms, N.M. / Kim, J.J.
History
DepositionOct 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 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

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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)35,9608
Polymers34,8872
Non-polymers1,0736
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.659, 91.659, 85.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 17443.580 Da / Num. of mol.: 2 / Mutation: N31Q, N57Q, N68Q, N87Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: M6PR / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-TN-5B1-4 / References: UniProt: P11456
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M cacodylate, 25% PEG5000MME, 0.2M ammonium sulfate, pH 6.5, vapor diffusion, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorDetector: CCD / Date: Sep 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 60846 / % possible obs: 94.1 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.081 / Χ2: 1.767 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.53.90.63747120.614174
1.5-1.566.20.48957540.69190.4
1.56-1.638.10.34861980.852197.2
1.63-1.728.80.27162640.818197.9
1.72-1.838.90.19562860.947198.2
1.83-1.9790.12863451.226198.8
1.97-2.1790.09163981.712199.3
2.17-2.489.10.07464842.155199.7
2.48-3.129.10.0665472.854199.8
3.12-307.90.05958584.912185.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
RefinementResolution: 1.45→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.237 4334 5.4 %
Rwork0.219 --
obs-60846 89.2 %
Solvent computationBsol: 48.196 Å2
Displacement parametersBiso mean: 17.972 Å2
Baniso -1Baniso -2Baniso -3
1--0.567 Å20 Å20 Å2
2---0.567 Å20 Å2
3---1.133 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 62 346 2774
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1991.5
X-RAY DIFFRACTIONc_scbond_it2.2012
X-RAY DIFFRACTIONc_mcangle_it1.9192
X-RAY DIFFRACTIONc_scangle_it3.2732.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2m6p.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4carbohydrate.param
X-RAY DIFFRACTION5ion.param

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