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- PDB-5mri: Crystal structure of the Vps10p domain of human sortilin/NTS3 in ... -

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Basic information

Entry
Database: PDB / ID: 5mri
TitleCrystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 18
ComponentsSortilin
KeywordsSIGNALING PROTEIN / Vps10p / Receptor / Sortilin
Function / homology
Function and homology information


neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / 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 ...neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / 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 / nerve growth factor binding / protein targeting to lysosome / trans-Golgi network transport vesicle / clathrin-coated vesicle / Golgi cisterna membrane / Golgi Associated Vesicle Biogenesis / 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 / endocytosis / regulation of gene expression / cytoplasmic vesicle / nuclear membrane / early endosome / lysosome / endosome membrane / G protein-coupled receptor signaling pathway / lysosomal membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / membrane / plasma membrane / cytosol
Similarity search - Function
Sortilin Vps10-D, 10CC-a domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #270 / VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 / : / Complement Module; domain 1 ...Sortilin Vps10-D, 10CC-a domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #270 / VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 / : / Complement Module; domain 1 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Ribbon / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAndersen, J.L. / Strandbygaard, D. / Thirup, S.
Funding support Denmark, 2items
OrganizationGrant numberCountry
DanScatt: the Danish Centre for the Use of Synchrotron X-ray and Neutron Facilities Denmark
European Community Seventh Framework Programme under BioStruct-X283570 Denmark
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: The identification of novel acid isostere based inhibitors of the VPS10P family sorting receptor Sortilin.
Authors: Andersen, J.L. / Lindberg, S. / Langgard, M. / Maltas, P.J. / Ronn, L.C.B. / Bundgaard, C. / Strandbygaard, D. / Thirup, S. / Watson, S.P.
History
DepositionDec 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2355
Polymers77,7911
Non-polymers1,4444
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint24 kcal/mol
Surface area31020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.296, 81.058, 105.690
Angle α, β, γ (deg.)90.00, 131.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1213-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sortilin / 100 kDa NT receptor / Glycoprotein 95 / Gp95 / Neurotensin receptor 3 / NTR3


Mass: 77790.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORT1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q99523

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Sugars , 3 types, 3 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.: 1 / 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.: 1 / 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 , 2 types, 348 molecules

#5: Chemical ChemComp-Q9Y / ~{N}-methyl-3-(3-methylbutyl)-5-oxidanyl-1,2,3-triazole-4-carboxamide


Mass: 212.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H16N4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.1 M HEPES-Tris pH 7.3 0.4 M Sodium malonate 6 % (V/V) glycerol 26 % (w/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2→64 Å / Num. obs: 67029 / % possible obs: 98.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 35.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.66 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F6K

3f6k


Resolution: 2→43.915 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.07
RfactorNum. reflection% reflection
Rfree0.219 2009 3 %
Rwork0.1951 --
obs0.1958 67019 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→43.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 96 347 5655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035483
X-RAY DIFFRACTIONf_angle_d0.7617456
X-RAY DIFFRACTIONf_dihedral_angle_d16.0073243
X-RAY DIFFRACTIONf_chiral_restr0.051828
X-RAY DIFFRACTIONf_plane_restr0.008951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30651490.31544627X-RAY DIFFRACTION99
2.05-2.10540.35461430.28784616X-RAY DIFFRACTION99
2.1054-2.16740.25681400.25684658X-RAY DIFFRACTION99
2.1674-2.23730.2891450.24264647X-RAY DIFFRACTION99
2.2373-2.31730.24561380.23194634X-RAY DIFFRACTION99
2.3173-2.41010.23771440.22844642X-RAY DIFFRACTION99
2.4101-2.51980.27481440.21984652X-RAY DIFFRACTION99
2.5198-2.65260.2481390.21924644X-RAY DIFFRACTION98
2.6526-2.81880.27911490.21054618X-RAY DIFFRACTION99
2.8188-3.03630.21421420.20554650X-RAY DIFFRACTION98
3.0363-3.34180.20961460.19454633X-RAY DIFFRACTION98
3.3418-3.82510.21951360.17334621X-RAY DIFFRACTION98
3.8251-4.81830.16171470.15444608X-RAY DIFFRACTION97
4.8183-43.92570.18931470.17574760X-RAY DIFFRACTION98
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)
12.80830.5145-0.32876.1883-0.77133.39880.02740.13460.3126-0.1730.10950.2513-0.364-0.7009-0.17720.29480.1596-0.02670.62370.00040.3515-39.1516-53.994317.0717
22.2392-0.2641-0.41220.5616-0.11290.5398-0.13470.2749-0.3575-0.0395-0.01010.06920.1908-0.19360.15330.3673-0.04190.03590.4044-0.09240.3637-36.9777-80.376324.5792
32.70460.7106-0.59622.78330.59361.9507-0.2452-0.1244-0.54520.1578-0.0893-0.21820.28280.39330.24040.34380.11760.08070.33030.10580.4726-9.4139-87.361530.927
41.842-0.3924-0.71032.0674-0.21592.12450.0756-0.22170.0740.1094-0.07-0.1278-0.20250.3067-0.00620.2219-0.0474-0.02790.3314-00.1884-8.1813-58.130429.5231
53.0928-0.3255-0.49370.65630.1612.04150.17620.24840.3184-0.0016-0.05230.0448-0.3249-0.342-0.13250.4020.06320.02330.36490.05160.3101-23.9818-49.64715.5103
61.6942-2.47532.8753.5524-4.16024.8197-0.03880.0538-0.14110.14-0.3336-0.28880.05190.52390.29290.5230.10510.02080.82060.14410.538811.7932-75.343221.1654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 238 )
3X-RAY DIFFRACTION3chain 'A' and (resid 239 through 317 )
4X-RAY DIFFRACTION4chain 'A' and (resid 318 through 470 )
5X-RAY DIFFRACTION5chain 'A' and (resid 471 through 626 )
6X-RAY DIFFRACTION6chain 'A' and (resid 627 through 715 )

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