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- PDB-1q25: Crystal structure of N-terminal 3 domains of CI-MPR -

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Basic information

Entry
Database: PDB / ID: 1q25
TitleCrystal structure of N-terminal 3 domains of CI-MPR
Componentscation-independent mannose 6-phosphate receptor
KeywordsPROTEIN TRANSPORT / SUGAR BINDING PROTEIN / P-lectin / receptor / mannose 6-phosphate
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsOlson, L.J. / Dahms, N.M. / Kim, J.-J.P.
CitationJournal: Embo J. / Year: 2004
Title: Structure of uPAR, plasminogen, and sugar-binding sites of the 300 kDa mannose 6-phosphate receptor
Authors: Olson, L.J. / Yammani, R.D. / Dahms, N.M. / Kim, J.-J.P.
History
DepositionJul 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cation-independent mannose 6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0464
Polymers47,6181
Non-polymers1,4273
Water6,575365
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.157, 84.746, 96.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein cation-independent mannose 6-phosphate receptor / CI / Man-6-P receptor / CI-MPR / Insulin-like growth factor II receptor / 300 kDa mannose 6- ...CI / Man-6-P receptor / CI-MPR / Insulin-like growth factor II receptor / 300 kDa mannose 6-phosphate receptor / MPR 300 / MPR300


Mass: 47618.461 Da / Num. of mol.: 1 / Fragment: N-terminal 3 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: IGF2R / Cell (production host): 5B1-4 cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P08169
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 47.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.35
Details: 25% PEG 4000, 0.1M sodium cacodylate,150 MM NACL, 50 mM IMIDAZOLE (PH=6.5), 10 MM MANGANESE CHLORIDE, 5 MM BETA-GLYCEROPHOSPHATE, 10mM mannose 6-phosphate, pH 6.35, VAPOR DIFFUSION, SITTING ...Details: 25% PEG 4000, 0.1M sodium cacodylate,150 MM NACL, 50 mM IMIDAZOLE (PH=6.5), 10 MM MANGANESE CHLORIDE, 5 MM BETA-GLYCEROPHOSPHATE, 10mM mannose 6-phosphate, pH 6.35, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 128 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 22, 2002 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→19.94 Å / Num. all: 51090 / Num. obs: 51090 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.7 Å2 / Limit h max: 34 / Limit h min: 0 / Limit k max: 48 / Limit k min: 0 / Limit l max: 51 / Limit l min: 0 / Observed criterion F max: 517618.99 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.75→1.81 Å / % possible all: 29.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
RESOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→19.94 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2820 6.9 %random
Rwork0.235 ---
all-46967 --
obs-40876 87.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 45.1504 Å2 / ksol: 0.364651 e/Å3
Displacement parametersBiso max: 85.32 Å2 / Biso mean: 34.19 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.615 Å20 Å20 Å2
2--3.453 Å20 Å2
3----4.068 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.33 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 95 365 3763
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg26.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.72
X-RAY DIFFRACTIONx_mcbond_it1.621.5
X-RAY DIFFRACTIONx_scbond_it2.3722
X-RAY DIFFRACTIONx_mcangle_it2.6662
X-RAY DIFFRACTIONx_scangle_it3.4162.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.3821706.50.3524640.0295779263445.6
1.88-1.980.3752716.60.3338170.0235809408870.4
1.98-2.10.3473997.70.28747640.0175813516388.8
2.1-2.270.31138870.26151740.0165836556295.3
2.27-2.490.3113896.80.24653040.0165846569397.4
2.49-2.860.3153886.70.24453880.0165850577698.7
2.86-3.590.2683956.70.22255030.0135935589899.4
3.59-19.940.2374206.90.20656420.0126132606298.9

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