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- PDB-6z30: Human cation-independent mannose 6-phosphate/ IGF2 receptor domai... -

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Basic information

Entry
Database: PDB / ID: 6z30
TitleHuman cation-independent mannose 6-phosphate/ IGF2 receptor domains 9-10
ComponentsCation-independent mannose-6-phosphate receptor
KeywordsSUGAR BINDING PROTEIN / Mannose 6-phosphate / Cation-independent mannose 6-phosphate receptor / Insulin-like growth factor 2 receptor / P-type lectin
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host 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 / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / Cargo recognition for clathrin-mediated endocytosis / late endosome / Clathrin-mediated endocytosis / signaling receptor activity / 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: 1.5 Å
AuthorsBochel, A.J. / Williams, C. / Crump, M.P.
Funding support United Kingdom, 3items
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
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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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 1.3May 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7202
Polymers33,6471
Non-polymers1,0731
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Confirmed dimerisation mechanism through N-linked glycan, mass spectrometry, ESI-MS confirmed protein of interest and glycosylation status
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint21 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.360, 55.830, 132.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 33646.758 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: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-e1_e3-f1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M SPG buffer (succinic acid, sodium dihydrogen phosphate monohydrate, glycine) pH 9, 25 % PEG 1500

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→51.46 Å / Num. obs: 48880 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 21.15 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.12
Reflection shellResolution: 1.5→1.81 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3040 / CC1/2: 0.744 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
xia20.5.902data reduction
DIALS1.14data scaling
PHASER2.8.2phasing
Coot0.8.9.2model building
PHENIX1.17.1-3660model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology models

Resolution: 1.5→51.46 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34
RfactorNum. reflection% reflection
Rfree0.2284 2446 5 %
Rwork0.1991 --
obs0.1977 48877 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→51.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 72 439 2732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052348
X-RAY DIFFRACTIONf_angle_d0.9233185
X-RAY DIFFRACTIONf_dihedral_angle_d6.001363
X-RAY DIFFRACTIONf_chiral_restr0.051360
X-RAY DIFFRACTIONf_plane_restr0.005406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.32041430.30024805X-RAY DIFFRACTION99.9
1.55-1.560.31171530.30072683X-RAY DIFFRACTION100
1.56-1.60.32181470.28862688X-RAY DIFFRACTION100
1.6-1.640.27921440.27892683X-RAY DIFFRACTION100
1.64-1.680.32521520.27862700X-RAY DIFFRACTION100
1.68-1.730.38031180.30822705X-RAY DIFFRACTION100
1.73-1.790.33091282703X-RAY DIFFRACTION100
1.79-1.850.33731410.30282741X-RAY DIFFRACTION100
1.85-1.930.27741380.21642702X-RAY DIFFRACTION100
1.93-2.020.22641630.19362701X-RAY DIFFRACTION100
2.02-2.120.20991480.19032698X-RAY DIFFRACTION100
2.12-2.260.25081640.18742708X-RAY DIFFRACTION100
2.26-2.430.24861360.18342750X-RAY DIFFRACTION100
2.43-2.670.22451390.19292762X-RAY DIFFRACTION100
2.67-3.060.21111430.18972768X-RAY DIFFRACTION100
3.06-3.860.17821430.15632797X-RAY DIFFRACTION100
3.86-51.460.1771460.1642970X-RAY DIFFRACTION100
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)
11.69310.7349-0.83291.1207-0.62781.58750.0563-0.0590.06670.06310.00340.0285-0.10410.0187-0.07360.14710.00750.00870.10780.0230.1288-7.420129.595458.379
21.69160.34940.45411.12480.83451.7049-0.0328-0.0021-0.09920.08770.0128-0.04590.0250.09920.04220.14640.00820.00380.13910.00220.12378.536826.09132.1759
35.03020.35220.88071.15190.42991.12870.08950.4403-0.0872-0.1433-0.09720.00090.06980.07460.01020.20810.0392-0.00560.2166-0.03410.15059.982222.822822.8282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1225 through 1360 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1361 through 1444 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1445 through 1509 )

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