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- PDB-5nnj: Dimer structure of Sortilin ectodomain crystal form 3, 4.0 Angstrom -

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Basic information

Entry
Database: PDB / ID: 5nnj
TitleDimer structure of Sortilin ectodomain crystal form 3, 4.0 Angstrom
ComponentsSortilin
KeywordsTRANSPORT PROTEIN / transport receptor / VPS10 domain
Function / homology
Function and homology information


neurotensin receptor activity, non-G protein-coupled / myotube differentiation / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / retromer complex binding / maintenance of synapse structure / Golgi to endosome transport / nerve growth factor receptor activity / Golgi to lysosome transport / vesicle organization ...neurotensin receptor activity, non-G protein-coupled / myotube differentiation / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / retromer complex binding / maintenance of synapse structure / Golgi to endosome transport / nerve growth factor receptor activity / Golgi to lysosome 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 / clathrin-coated vesicle / negative regulation of fat cell differentiation / Golgi cisterna membrane / endosome to lysosome transport / glucose import / neurotrophin TRK receptor signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / neuropeptide signaling pathway / clathrin-coated pit / ossification / response to insulin / cytoplasmic vesicle membrane / endocytosis / cytoplasmic vesicle / regulation of gene expression / nuclear membrane / lysosome / early endosome / endosome membrane / G protein-coupled receptor signaling pathway / lysosomal membrane / dendrite / neuronal cell body / 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: 4 Å
AuthorsLeloup, N.O.L. / Janssen, B.J.C.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
NWO723.012.002 Netherlands
Eu Marie Curie317371 Netherlands
CitationJournal: Nat Commun / Year: 2017
Title: Low pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release.
Authors: Leloup, N. / Lossl, P. / Meijer, D.H. / Brennich, M. / Heck, A.J.R. / Thies-Weesie, D.M.E. / Janssen, B.J.C.
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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_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

Downloads & links

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Assembly

Deposited unit
A: Sortilin
B: Sortilin
D: Sortilin
C: Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,03316
Polymers325,4564
Non-polymers5,57712
Water0
1
A: Sortilin
B: Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,5178
Polymers162,7282
Non-polymers2,7896
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint22 kcal/mol
Surface area53860 Å2
MethodPISA
2
D: Sortilin
C: Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,5178
Polymers162,7282
Non-polymers2,7896
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint21 kcal/mol
Surface area54550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.320, 151.820, 162.740
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.: 4
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.: 8
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: 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.: 4
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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.18 M Magnesium formate dihydrate pH 7.0, 18% PEG 3350 (w/v), 1 mM CaCl2 and 1 mM GSH (L-Glutathione reduced) & GSSG (L-Glutathione oxidized), final pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97599 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97599 Å / Relative weight: 1
ReflectionResolution: 4→71.72 Å / Num. obs: 32164 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03936 / Rpim(I) all: 0.03936 / Rrim(I) all: 0.05567 / Net I/σ(I): 7.7
Reflection shellResolution: 4→4.143 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4076 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 3145 / CC1/2: 0.789 / Rpim(I) all: 0.4076 / Rrim(I) all: 0.5765 / % possible all: 99.71

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Processing

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

5nmt


Resolution: 4→71.719 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1433 4.47 %
Rwork0.1863 --
obs0.1892 32054 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→71.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20362 0 368 0 20730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421263
X-RAY DIFFRACTIONf_angle_d1.28128850
X-RAY DIFFRACTIONf_dihedral_angle_d12.7677800
X-RAY DIFFRACTIONf_chiral_restr0.0713199
X-RAY DIFFRACTIONf_plane_restr0.0063677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.1430.34381330.27223004X-RAY DIFFRACTION100
4.143-4.30890.3352910.22293072X-RAY DIFFRACTION100
4.3089-4.5050.2654880.19693069X-RAY DIFFRACTION100
4.505-4.74240.26731240.16923049X-RAY DIFFRACTION99
4.7424-5.03950.24751860.1542989X-RAY DIFFRACTION100
5.0395-5.42850.23511720.16483027X-RAY DIFFRACTION100
5.4285-5.97450.24231440.17443048X-RAY DIFFRACTION100
5.9745-6.83840.26341840.1883035X-RAY DIFFRACTION100
6.8384-8.61340.2891430.19243111X-RAY DIFFRACTION100
8.6134-71.73010.20871680.18443217X-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)
11.38150.0373-0.12696.76631.05582.5474-0.10930.1271-0.0086-0.68530.2910.1947-0.1670.0187-0.20161.0508-0.1042-0.01931.23690.05520.9328152.6712212.583519.174
21.4787-0.32350.2874.86730.85792.2406-0.0008-0.1868-0.00591.11060.4218-0.5840.37940.3182-0.3641.35660.2775-0.07181.3276-0.22781.1582165.9101226.157555.6126
32.7215-0.8469-0.55125.6856-0.47652.92390.37420.1134-0.31590.0489-0.33380.5865-0.0071-0.7080.03781.181-0.0743-0.10551.4755-0.10090.8426138.0517199.0165140.4624
41.17250.2530.11294.603-0.98842.9073-0.02690.32740.1524-0.69740.0519-0.25560.7023-0.2266-0.03771.71820.0144-0.07671.3646-0.02621.1268142.3424212.5467101.325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 53 through 1651)
2X-RAY DIFFRACTION2(chain 'B' and resid 53 through 1651)
3X-RAY DIFFRACTION3(chain 'C' and resid 53 through 1651)
4X-RAY DIFFRACTION4(chain 'D' and resid 53 through 1651)

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