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- PDB-6z31: Human cation-independent mannose 6-phosphate/ IGF2 receptor domain 8 -

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Basic information

Entry
Database: PDB / ID: 6z31
TitleHuman cation-independent mannose 6-phosphate/ IGF2 receptor domain 8
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 / 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: 2.56 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)30,2836
Polymers30,1662
Non-polymers1174
Water1,838102
1
A: Cation-independent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1413
Polymers15,0831
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cation-independent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1413
Polymers15,0831
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.555, 45.537, 70.275
Angle α, β, γ (deg.)90.00, 116.36, 90.00
Int Tables number4
Space group name H-MP1211

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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: 15082.927 Da / Num. of mol.: 2
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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5 M Ammonium sulphate, 0.1 M Tris pH 8.5, 12 % glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.56→36.02 Å / Num. obs: 12121 / % possible obs: 98.98 % / Redundancy: 4.7 % / Biso Wilson estimate: 40.52 Å2 / CC1/2: 0.975 / Net I/σ(I): 5.59
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 1170 / CC1/2: 0.686 / % possible all: 95.82

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Processing

Software
NameVersionClassification
PHENIX(1.18_3855: ???)refinement
xia20.5.902data reduction
DIALS1.14data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Domain 10 from the crystal structure of cation-independent mannose 6-phosphate receptor domains 9-10 (separate deposition)

Resolution: 2.56→36.02 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 --
Rwork0.2234 --
obs-12116 98.98 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→36.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 4 102 2201
LS refinement shellResolution: 2.56→2.65 Å
RfactorNum. reflection% reflection
Rfree0.3839 --
Rwork0.271 1169 -
obs--95.82 %
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)
10.5614-0.54520.87061.8258-0.53793.1967-0.15750.00440.0310.251-0.0318-0.22730.1658-0.38120.13060.3577-0.0437-0.01290.188-0.03820.168218.7934-22.872518.0476
21.9297-0.2511-0.97782.20540.74742.7108-0.1208-0.1426-0.11130.41580.0328-0.19690.0887-0.01190.02290.29610.0265-0.04750.14850.02040.119524.456-26.91518.876
31.19020.04820.77751.6706-0.23881.6423-0.0314-0.18750.14930.0433-0.0527-0.09910.0353-0.15870.12810.27950.0063-0.03840.1291-0.01490.246312.753-8.61486.5502
42.51341.033-0.68773.1010.21441.2707-0.11810.3292-0.0226-0.56970.02620.0566-0.1059-0.24920.08760.2444-0.0074-0.06730.195-0.00270.176114.1372-5.64750.0314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1081 through 1132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1133 through 1220 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1081 through 1138 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1139 through 1220 )

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