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- PDB-6v02: N-terminal 5 domains of CI-MPR -

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Basic information

Entry
Database: PDB / ID: 6v02
TitleN-terminal 5 domains of CI-MPR
ComponentsCation-independent mannose-6-phosphate receptor
KeywordsSUGAR BINDING PROTEIN / Lectin / receptor / protein transport
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / membrane / identical protein binding / 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 / 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. ...Cation-independent mannose-6-phosphate receptor repeat / 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
Similarity search - Domain/homology
Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsOlson, L.J. / Dahms, N.M. / Kim, J.-J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1DK042667 United States
CitationJournal: Commun Biol / Year: 2020
Title: Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor.
Authors: Olson, L.J. / Misra, S.K. / Ishihara, M. / Battaile, K.P. / Grant, O.C. / Sood, A. / Woods, R.J. / Kim, J.P. / Tiemeyer, M. / Ren, G. / Sharp, J.S. / Dahms, N.M.
History
DepositionNov 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)81,4212
Polymers81,2001
Non-polymers2211
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.780, 66.220, 124.530
Angle α, β, γ (deg.)90.00, 100.53, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cation-independent mannose-6-phosphate receptor / M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like growth factor 2 receptor / ...M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like growth factor 2 receptor / Insulin-like growth factor II receptor / IGF-II receptor / M6P/IGF2 receptor / M6P/IGF2R


Mass: 81199.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2R, MPRI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11717
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES pH 7.0, 30% Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→122.432 Å / Num. obs: 19610 / % possible obs: 91.1 % / Redundancy: 5 % / Biso Wilson estimate: 62.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.7
Reflection shellResolution: 2.46→2.76 Å / Redundancy: 3.9 % / Num. unique obs: 981 / CC1/2: 0.605 / % possible all: 58.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
autoPROCdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P8I

6p8i


Resolution: 2.46→35.91 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.853 / SU B: 43.069 / SU ML: 0.406 / Cross valid method: THROUGHOUT / ESU R: 2.595 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.30778 996 5.1 %RANDOM
Rwork0.24017 ---
obs0.24356 18604 66.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.091 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0 Å23.71 Å2
2---2.43 Å20 Å2
3---2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.46→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 14 74 4570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194604
X-RAY DIFFRACTIONr_bond_other_d0.0010.024113
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.8866243
X-RAY DIFFRACTIONr_angle_other_deg0.9492.9349565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6645561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56423.942208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15115754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8441527
X-RAY DIFFRACTIONr_chiral_restr0.0670.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02951
X-RAY DIFFRACTIONr_mcbond_it1.1684.4572280
X-RAY DIFFRACTIONr_mcbond_other1.1684.4572279
X-RAY DIFFRACTIONr_mcangle_it2.1456.6762829
X-RAY DIFFRACTIONr_mcangle_other2.1456.6762830
X-RAY DIFFRACTIONr_scbond_it0.8364.5332324
X-RAY DIFFRACTIONr_scbond_other0.8364.5362325
X-RAY DIFFRACTIONr_scangle_other1.5586.763415
X-RAY DIFFRACTIONr_long_range_B_refined4.13352.6995151
X-RAY DIFFRACTIONr_long_range_B_other4.11452.6725142
LS refinement shellResolution: 2.463→2.527 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.389 66 -
Rfree-1 -
obs--3.06 %
Refinement TLS params.Method: refined / Origin x: 17.509 Å / Origin y: 0.381 Å / Origin z: 31.384 Å
111213212223313233
T0.2308 Å2-0.044 Å2-0.0839 Å2-0.1345 Å20.0182 Å2--0.0466 Å2
L2.5371 °20.0887 °21.9859 °2-0.9709 °2-0.0305 °2--3.5122 °2
S0.0176 Å °-0.1738 Å °-0.121 Å °0.1443 Å °-0.0199 Å °-0.0268 Å °0.1012 Å °-0.1318 Å °0.0023 Å °

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