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- PDB-5znn: Crystal structure of ligand-free form of the Vps10 ectodomain of ... -

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Basic information

Entry
Database: PDB / ID: 5znn
TitleCrystal structure of ligand-free form of the Vps10 ectodomain of Sortilin
ComponentsSortilin
KeywordsPROTEIN TRANSPORT / Cytokine trafficking
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 / Golgi to endosome transport / nerve growth factor receptor activity / 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 / Golgi to endosome transport / nerve growth factor receptor activity / 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 / negative regulation of fat cell differentiation / 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 / regulation of gene expression / nuclear membrane / lysosome / early endosome / endosome membrane / lysosomal membrane / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / 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
ACETATE ION / Sortilin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.448 Å
AuthorsYabe-Wada, T. / Unno, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
CitationJournal: FEBS Lett. / Year: 2018
Title: Crystal structure of the ligand-free form of the Vps10 ectodomain of dimerized Sortilin at acidic pH
Authors: Yabe-Wada, T. / Matsuba, S. / Unno, M. / Onai, N.
History
DepositionApr 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 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_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,58119
Polymers151,7962
Non-polymers3,78517
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-29 kcal/mol
Surface area53420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.264, 138.496, 146.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 84 through 86 or resid 88...
21(chain B and (resid 84 through 86 or resid 88...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 84 through 86 or resid 88...A84 - 86
121(chain A and (resid 84 through 86 or resid 88...A88 - 116
131(chain A and (resid 84 through 86 or resid 88...A118 - 184
141(chain A and (resid 84 through 86 or resid 88...A186 - 218
151(chain A and (resid 84 through 86 or resid 88...A224 - 228
161(chain A and (resid 84 through 86 or resid 88...A247 - 275
171(chain A and (resid 84 through 86 or resid 88...A280 - 340
181(chain A and (resid 84 through 86 or resid 88...A273 - 278
191(chain A and (resid 84 through 86 or resid 88...A350 - 351
1101(chain A and (resid 84 through 86 or resid 88...A359 - 367
1111(chain A and (resid 84 through 86 or resid 88...A365
1121(chain A and (resid 84 through 86 or resid 88...A83 - 738
1131(chain A and (resid 84 through 86 or resid 88...A83 - 738
1141(chain A and (resid 84 through 86 or resid 88...A83 - 738
1151(chain A and (resid 84 through 86 or resid 88...A83 - 738
1161(chain A and (resid 84 through 86 or resid 88...A83 - 738
211(chain B and (resid 84 through 86 or resid 88...B84 - 86
221(chain B and (resid 84 through 86 or resid 88...B88 - 116
231(chain B and (resid 84 through 86 or resid 88...B118 - 184
241(chain B and (resid 84 through 86 or resid 88...B224 - 228
251(chain B and (resid 84 through 86 or resid 88...B83 - 739
261(chain B and (resid 84 through 86 or resid 88...B247 - 270
271(chain B and (resid 84 through 86 or resid 88...B83 - 739
281(chain B and (resid 84 through 86 or resid 88...B280 - 34
291(chain B and (resid 84 through 86 or resid 88...B350 - 357
2101(chain B and (resid 84 through 86 or resid 88...B359 - 441
2111(chain B and (resid 84 through 86 or resid 88...B444
2121(chain B and (resid 84 through 86 or resid 88...B45
2131(chain B and (resid 84 through 86 or resid 88...B47 - 486
2141(chain B and (resid 84 through 86 or resid 88...B488 - 535
2151(chain B and (resid 84 through 86 or resid 88...B537 - 578
2161(chain B and (resid 84 through 86 or resid 88...B0
2171(chain B and (resid 84 through 86 or resid 88...B582 - 602
2181(chain B and (resid 84 through 86 or resid 88...B603
2191(chain B and (resid 84 through 86 or resid 88...B83 - 739
2201(chain B and (resid 84 through 86 or resid 88...B83 - 739
2211(chain B and (resid 84 through 86 or resid 88...B83 - 739
2221(chain B and (resid 84 through 86 or resid 88...B83 - 739
2231(chain B and (resid 84 through 86 or resid 88...B83 - 739

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sortilin / Neurotensin receptor 3 / mNTR3


Mass: 75897.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sort1 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6PHU5

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Sugars , 3 types, 8 molecules

#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.: 4 / Source method: obtained synthetically
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: obtained synthetically
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.: 3 / Source method: obtained synthetically / 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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Non-polymers , 3 types, 443 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Na
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 23% (w/v) polyethylene glycol monomethyl ether 550 (Sigma), 0.4 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.448→50 Å / Num. obs: 60757 / % possible obs: 99.6 % / Redundancy: 4.6 % / Net I/σ(I): 22.6
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2997 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PO7

4po7


Resolution: 2.448→38.607 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 2950 4.86 %
Rwork0.1796 57743 -
obs0.1814 60693 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.26 Å2 / Biso mean: 57.0296 Å2 / Biso min: 18.86 Å2
Refinement stepCycle: final / Resolution: 2.448→38.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10026 0 247 434 10707
Biso mean--80.83 49.36 -
Num. residues----1293
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5397X-RAY DIFFRACTION12.176TORSIONAL
12B5397X-RAY DIFFRACTION12.176TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.448-2.48810.29271360.23452674281098
2.4881-2.5310.29671510.215527232874100
2.531-2.5770.24971320.210927172849100
2.577-2.62660.2671280.208127082836100
2.6266-2.68020.26041560.205827212877100
2.6802-2.73840.26641340.213727102844100
2.7384-2.80210.26211390.209527232862100
2.8021-2.87210.32771380.217527432881100
2.8721-2.94980.25551450.209527042849100
2.9498-3.03650.24481620.198827192881100
3.0365-3.13450.24521200.201327572877100
3.1345-3.24650.27211500.200427292879100
3.2465-3.37640.24091490.203527452894100
3.3764-3.530.20681390.187227432882100
3.53-3.71590.21331370.178827592896100
3.7159-3.94850.21521250.168327752900100
3.9485-4.25310.18391480.151127552903100
4.2531-4.68040.17181290.132127952924100
4.6804-5.35610.15911470.138728022949100
5.3561-6.74230.20791430.172928312974100
6.7423-38.61180.18481420.19132910305298
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)
16.4101-1.8575-0.33042.03780.0230.8786-0.03470.0757-0.148-0.22310.03750.16540.1594-0.1005-0.00440.59650.0793-0.0520.37910.05330.2253.1777-1.3496-43.1072
20.6509-0.2063-0.6212.1741.1931.45080.07030.08720.2991-0.21380.0138-0.3621-0.11960.3183-0.1060.50680.0422-0.00550.44460.11670.415426.188417.4123-39.2777
31.32390.92810.15023.16110.24370.88850.02560.05920.2987-0.0696-0.01560.0671-0.2449-0.0118-0.02330.46950.063-0.01880.29930.07290.37881.361626.87-32.626
42.86910.84470.60342.37360.56161.37570.0039-0.27950.22780.1821-0.0420.2642-0.0874-0.19320.01240.38040.06850.04290.3158-0.00720.2263.82996.14911.8468
56.2209-2.3393-2.13024.08631.44591.61750.03160.06130.5876-0.29710.0396-0.5001-0.53340.2245-0.05440.3641-0.1028-0.04640.36670.02260.33633.380711.1536-2.8585
65.25860.23541.01432.6826-0.28422.16930.12440.33090.2588-0.2795-0.1531-0.28580.15190.2740.00680.25710.02770.0370.28310.07040.25826.5346-12.5278-17.4091
73.4346-0.0141-0.76231.8959-0.03751.63360.0328-0.2689-0.61890.0454-0.10260.13470.13080.0553-0.04250.2722-0.0327-0.0120.25570.08150.28416.9105-17.09-8.6869
84.62550.7974-0.70520.7548-0.290.11750.1761-0.915-1.0078-0.0356-0.1872-0.06020.20460.3138-0.03740.42020.01440.01060.66790.27180.68228.6506-24.9074-5.7739
92.05231.07450.65383.25852.07072.59820.3635-0.63450.2443-0.24870.3146-1.6217-0.08710.5631-0.36930.33850.05870.0860.79780.03221.064451.0267-13.357-9.4085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 193 )A83 - 193
2X-RAY DIFFRACTION2chain 'A' and (resid 194 through 392 )A194 - 392
3X-RAY DIFFRACTION3chain 'A' and (resid 393 through 738 )A393 - 738
4X-RAY DIFFRACTION4chain 'B' and (resid 83 through 231 )B83 - 231
5X-RAY DIFFRACTION5chain 'B' and (resid 232 through 354 )B232 - 354
6X-RAY DIFFRACTION6chain 'B' and (resid 355 through 482 )B355 - 482
7X-RAY DIFFRACTION7chain 'B' and (resid 483 through 639 )B483 - 639
8X-RAY DIFFRACTION8chain 'B' and (resid 640 through 683 )B640 - 683
9X-RAY DIFFRACTION9chain 'B' and (resid 684 through 739 )B684 - 739

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