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- PDB-6fg9: Mouse SORCS2 ectodomain (sortilin related VPS10 domain containing... -

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Basic information

Entry
Database: PDB / ID: 6fg9
TitleMouse SORCS2 ectodomain (sortilin related VPS10 domain containing receptor 2)
ComponentsVPS10 domain-containing receptor SorCS2
KeywordsAPOPTOSIS / SorCS2 / VPS10 / transport / sorting / Sortilin
Function / homology
Function and homology information


long-term synaptic depression / postsynaptic density membrane / intracellular protein transport / recycling endosome membrane / early endosome membrane / perikaryon / dendritic spine / postsynaptic density / intracellular membrane-bounded organelle / membrane ...long-term synaptic depression / postsynaptic density membrane / intracellular protein transport / recycling endosome membrane / early endosome membrane / perikaryon / dendritic spine / postsynaptic density / intracellular membrane-bounded organelle / membrane / plasma membrane / cytosol
Similarity search - Function
VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
VPS10 domain-containing receptor SorCS2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsLeloup, N.O.L. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Marie Curie FP7317371 Netherlands
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into SorCS2-Nerve Growth Factor complex formation.
Authors: Leloup, N. / Chataigner, L.M.P. / Janssen, B.J.C.
History
DepositionJan 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: VPS10 domain-containing receptor SorCS2
B: VPS10 domain-containing receptor SorCS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,66413
Polymers218,2312
Non-polymers2,43311
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint4 kcal/mol
Surface area94000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.815, 329.275, 131.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein VPS10 domain-containing receptor SorCS2


Mass: 109115.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sorcs2 / Production host: Homo sapiens (human) / References: UniProt: Q9EPR5
#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.: 11
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

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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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1 M Sodium chloride, 0.02 M Tris pH 7.5, 0.1 M Magnesium chloride hexahydrate and 11 % w/v PEG 1500, final pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 4→49.203 Å / Num. obs: 26077 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5
Reflection shellResolution: 4→4.26 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4652 / CC1/2: 0.35 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4SML, 1WGO, 4AQO

4sml

1wgo

4aqo


Resolution: 4.2→49.203 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2907 1163 5.2 %
Rwork0.2493 --
obs0.2514 22368 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.2→49.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14558 0 154 0 14712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215065
X-RAY DIFFRACTIONf_angle_d0.58620525
X-RAY DIFFRACTIONf_dihedral_angle_d9.0188975
X-RAY DIFFRACTIONf_chiral_restr0.0462364
X-RAY DIFFRACTIONf_plane_restr0.0052615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.3910.35711490.32792599X-RAY DIFFRACTION100
4.391-4.62240.34441270.28382632X-RAY DIFFRACTION100
4.6224-4.91170.31661490.26182617X-RAY DIFFRACTION100
4.9117-5.29060.30751650.25292619X-RAY DIFFRACTION100
5.2906-5.82220.34081410.26422632X-RAY DIFFRACTION100
5.8222-6.6630.32211360.27822653X-RAY DIFFRACTION100
6.663-8.38790.31281500.26142664X-RAY DIFFRACTION100
8.3879-49.20650.22871460.21082789X-RAY DIFFRACTION99

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