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- PDB-5nni: Dimer structure of Sortilin ectodomain crystal form 2, 3.2 Angstrom -

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Basic information

Entry
Database: PDB / ID: 5nni
TitleDimer structure of Sortilin ectodomain crystal form 2, 3.2 Angstrom
ComponentsSortilin
KeywordsTRANSPORT PROTEIN / VPS10 domain / transport receptor / internalization / 10 bladed beta-propeller
Function / homology
Function and homology information


neurotensin receptor activity, non-G protein-coupled / Golgi to lysosome transport / myotube differentiation / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / maintenance of synapse structure / retromer complex binding / nerve growth factor receptor activity / Golgi to endosome transport / vesicle organization ...neurotensin receptor activity, non-G protein-coupled / Golgi to lysosome transport / myotube differentiation / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / maintenance of synapse structure / retromer complex binding / nerve growth factor receptor activity / Golgi to endosome transport / vesicle organization / endosome transport via multivesicular body sorting pathway / Golgi Associated Vesicle Biogenesis / nerve growth factor binding / protein targeting to lysosome / trans-Golgi network transport vesicle / positive regulation of epithelial cell apoptotic process / Golgi cisterna membrane / endosome to lysosome transport / negative regulation of fat cell differentiation / D-glucose import / neurotrophin TRK receptor signaling pathway / neuropeptide signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / clathrin-coated pit / ossification / response to insulin / cytoplasmic vesicle membrane / endocytosis / regulation of gene expression / nuclear membrane / early endosome / lysosome / endosome membrane / lysosomal membrane / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / 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 / : / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsLeloup, N.O.L. / Janssen, B.J.C.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
NWO723.012.002 Netherlands
Marie Curie317371 Netherlands
CitationJournal: Nat Commun / Year: 2017
Title: Low pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release.
Authors: Nadia Leloup / Philip Lössl / Dimphna H Meijer / Martha Brennich / Albert J R Heck / Dominique M E Thies-Weesie / Bert J C Janssen /
Abstract: Low pH-induced ligand release and receptor recycling are important steps for endocytosis. The transmembrane protein sortilin, a β-propeller containing endocytosis receptor, internalizes a diverse ...Low pH-induced ligand release and receptor recycling are important steps for endocytosis. The transmembrane protein sortilin, a β-propeller containing endocytosis receptor, internalizes a diverse set of ligands with roles in cell differentiation and homeostasis. The molecular mechanisms of pH-mediated ligand release and sortilin recycling are unresolved. Here we present crystal structures that show the sortilin luminal segment (s-sortilin) undergoes a conformational change and dimerizes at low pH. The conformational change, within all three sortilin luminal domains, provides an altered surface and the dimers sterically shield a large interface while bringing the two s-sortilin C-termini into close proximity. Biophysical and cell-based assays show that members of two different ligand families, (pro)neurotrophins and neurotensin, preferentially bind the sortilin monomer. This indicates that sortilin dimerization and conformational change discharges ligands and triggers recycling. More generally, this work may reveal a double mechanism for low pH-induced ligand release by endocytosis receptors.
History
DepositionApr 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: 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.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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: Sortilin
B: Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,3558
Polymers162,7282
Non-polymers2,6266
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS, light scattering, mass spectrometry, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint20 kcal/mol
Surface area53350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.842, 137.170, 147.560
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 Sortilin / Neurotensin receptor 3 / mNTR3


Mass: 81364.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sort1 / Production host: Homo sapiens (human) / References: UniProt: Q6PHU5
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 2
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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M NH4Cl, 1 mM CaCl2 and 20% PEG 3350 (w/v), pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 3.21→62.2 Å / Num. obs: 27112 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Net I/σ(I): 14.1
Reflection shellResolution: 3.21→3.325 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1578 / Mean I/σ(I) obs: 4.37 / Num. unique obs: 2654 / CC1/2: 0.945 / Rpim(I) all: 0.1578 / % possible all: 99.59

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NMT

5nmt


Resolution: 3.21→62.195 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.38
RfactorNum. reflection% reflection
Rfree0.2548 1365 5.04 %
Rwork0.2274 --
obs0.2288 27058 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.21→62.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10237 0 173 0 10410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210681
X-RAY DIFFRACTIONf_angle_d0.68614495
X-RAY DIFFRACTIONf_dihedral_angle_d10.4616304
X-RAY DIFFRACTIONf_chiral_restr0.061603
X-RAY DIFFRACTIONf_plane_restr0.0031852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.32480.3681340.34492521X-RAY DIFFRACTION100
3.3248-3.45790.28751220.28192545X-RAY DIFFRACTION100
3.4579-3.61520.27771570.25582534X-RAY DIFFRACTION100
3.6152-3.80580.27771760.25842503X-RAY DIFFRACTION100
3.8058-4.04420.27241370.2532517X-RAY DIFFRACTION100
4.0442-4.35640.27351300.21842552X-RAY DIFFRACTION99
4.3564-4.79470.19551260.18092595X-RAY DIFFRACTION100
4.7947-5.48810.20841180.18882579X-RAY DIFFRACTION99
5.4881-6.9130.26031310.22132614X-RAY DIFFRACTION99
6.913-62.20680.25351340.22882733X-RAY DIFFRACTION99
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)
12.56240.04130.4481.74350.00652.56510.1116-0.1437-0.1176-0.0144-0.19370.05090.3773-0.12260.09150.42040.04250.01720.3728-0.10530.403623.38121.6548-7.0509
21.5627-0.12990.72581.5272-0.16392.18090.14270.3274-0.3024-0.0812-0.07050.02470.66540.2976-0.04051.00160.17520.04310.6955-0.21950.575429.9966-14.0397-35.9775
32.2951-0.74810.84321.3452-0.11591.0672-0.1345-0.69920.83950.1191-0.24540.4812-0.342-0.57310.21270.60170.1032-0.01611.1724-0.45431.06246.24319.5375-5.1327
40.427-0.03580.58291.64930.04831.17870.40340.3642-0.3928-0.03440.09970.08950.9320.3181-0.43021.83570.1761-0.00380.9683-0.27711.367530.6025-38.0934-38.6193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 53 through 572)
2X-RAY DIFFRACTION2(chain 'B' and resid 53 through 572)
3X-RAY DIFFRACTION3(chain 'A' and resid 573 through 722)
4X-RAY DIFFRACTION4(chain 'B' and resid 573 through 722)

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