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- PDB-6z32: Human cation-independent mannose 6-phosphate/IGF2 receptor domain... -

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Basic information

Entry
Database: PDB / ID: 6z32
TitleHuman cation-independent mannose 6-phosphate/IGF2 receptor domains 7-11
ComponentsCation-independent mannose-6-phosphate receptor
KeywordsSUGAR BINDING PROTEIN / Cation-independent mannose 6-phosphate receptor / Insulin-like growth factor 2 receptor / Mannose 6-phosphate
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 / 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. ...Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / 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
Similarity search - Domain/homology
Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsBochel, A.J. / Williams, C. / McCoy, A.J. / Hoppe, H. / Winter, A.J. / Nicholls, R.D. / Harlos, K. / Jones, Y.E. / Berger, I. / Hassan, B. / Crump, M.P.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J014400/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009122/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Cancer Research UKC429/A9891 United Kingdom
CitationJournal: Structure / Year: 2020
Title: Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7-11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9.
Authors: Bochel, A.J. / Williams, C. / McCoy, A.J. / Hoppe, H.J. / Winter, A.J. / Nicholls, R.D. / Harlos, K. / Jones, E.Y. / Berger, I. / Hassan, A.B. / Crump, M.P.
History
DepositionMay 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_DOI ..._citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,5718
Polymers161,6662
Non-polymers2,9066
Water00
1
A: Cation-independent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2234
Polymers80,8331
Non-polymers1,3903
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cation-independent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3484
Polymers80,8331
Non-polymers1,5153
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.204, 139.204, 234.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 934 - 1646 / Label seq-ID: 22 - 734

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 80832.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ETGQLKHHHHHHEFTTTDTDQ are vector derived / Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2R, MPRI / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P11717
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_d2-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: 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.: 3
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
Has ligand of interestN
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: 3.75 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 1.6 M MgSO4, 10 mM mannose 6-phosphate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.05811 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05811 Å / Relative weight: 1
ReflectionResolution: 3.47→89.72 Å / Num. obs: 30224 / % possible obs: 98.55 % / Redundancy: 14.5 % / CC1/2: 0.997 / Net I/σ(I): 6.03
Reflection shellResolution: 3.47→3.59 Å / Redundancy: 14.9 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 2944 / CC1/2: 0.127 / % possible all: 98.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia20.5.902data reduction
DIALS1.14data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology models of D7, 8, 9, 10, Crystal structure of D11 (1GP0)

1gp0


Resolution: 3.47→89.72 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.913 / SU B: 105.945 / SU ML: 0.706 / Cross valid method: THROUGHOUT / ESU R Free: 0.628 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1493 4.9 %RANDOM
Rwork0.2607 ---
obs-30215 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 197.426 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 3.47→89.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10358 0 191 0 10549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310834
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179647
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.67514741
X-RAY DIFFRACTIONr_angle_other_deg1.2421.59622532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8625.1961379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03522.451514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22115.1831750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8111559
X-RAY DIFFRACTIONr_chiral_restr0.060.21447
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022236
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.74815.0895384
X-RAY DIFFRACTIONr_mcbond_other9.73915.095383
X-RAY DIFFRACTIONr_mcangle_it15.28822.6336695
X-RAY DIFFRACTIONr_mcangle_other15.28822.6336696
X-RAY DIFFRACTIONr_scbond_it10.34516.0545448
X-RAY DIFFRACTIONr_scbond_other10.34416.0545449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.28623.7498047
X-RAY DIFFRACTIONr_long_range_B_refined25.87641726
X-RAY DIFFRACTIONr_long_range_B_other25.87641727
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18066 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.47→3.59 Å
RfactorNum. reflection% reflection
Rfree0.4323 87 -
Rwork0.4212 2943 -
obs--98.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7235-0.74040.46262.0266-0.32670.83420.01270.14010.2854-0.0279-0.317-0.1668-0.17440.08650.30430.14040.03190.11290.0920.04080.5748175.506989.3958246.1218
20.6951-0.5342-0.01670.7613-0.02160.1551-0.0968-0.15480.23940.0504-0.0359-0.1685-0.20560.00890.13270.36580.1212-0.09170.2746-0.00090.6833170.4722100.3902223.3766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A934 - 1646
2X-RAY DIFFRACTION2B933 - 1646

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