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- PDB-4msl: Crystal structure of the Vps10p domain of human sortilin/NTS3 in ... -

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Basic information

Entry
Database: PDB / ID: 4msl
TitleCrystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF40431
ComponentsSortilin
KeywordsSIGNALING PROTEIN / proNGF / Alzheimer's disease / Beta-propeller / Asp-box repeat / Vps10p domain / 10CC domain / Receptor Sorting / Peptide binding / Protein binding / Membrane
Function / homology
Function and homology information


neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / 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 ...neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / 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 / nerve growth factor binding / protein targeting to lysosome / trans-Golgi network transport vesicle / clathrin-coated vesicle / negative regulation of fat cell differentiation / Golgi cisterna membrane / Golgi Associated Vesicle Biogenesis / 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 / endocytosis / cytoplasmic vesicle / regulation of gene expression / nuclear membrane / lysosome / early endosome / 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 / Wheat Germ Agglutinin (Isolectin 2); 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: 2.7 Å
AuthorsAndersen, J.L. / Strandbygaard, D. / Thirup, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor-ligand complex.
Authors: Andersen, J.L. / Schrder, T.J. / Christensen, S. / Strandbygard, D. / Pallesen, L.T. / Garcia-Alai, M.M. / Lindberg, S. / Langgard, M. / Eskildsen, J.C. / David, L. / Tagmose, L. / Simonsen, ...Authors: Andersen, J.L. / Schrder, T.J. / Christensen, S. / Strandbygard, D. / Pallesen, L.T. / Garcia-Alai, M.M. / Lindberg, S. / Langgard, M. / Eskildsen, J.C. / David, L. / Tagmose, L. / Simonsen, K.B. / Maltas, P.J. / Rnn, L.C. / de Jong, I.E. / Malik, I.J. / Egebjerg, J. / Karlsson, J.J. / Uppalanchi, S. / Sakumudi, D.R. / Eradi, P. / Watson, S.P. / Thirup, S.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6405
Polymers77,7911
Non-polymers1,8494
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.876, 79.165, 111.700
Angle α, β, γ (deg.)90.00, 127.27, 90.00
Int Tables number5
Space group name H-MC121

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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 / NT3 / NTR3


Mass: 77790.883 Da / Num. of mol.: 1 / Fragment: Vps10p domain (UNP residues 78-756)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORT1 / Plasmid: pCEP-pu / Cell (production host): Human Embryonic Kidney 293F cells / Production host: Homo Sapiens (human) / References: UniProt: Q99523

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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: 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

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Non-polymers , 3 types, 69 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-2ET / N-[(7-hydroxy-4-methyl-2-oxo-2H-chromen-8-yl)methyl]-L-leucine


Mass: 319.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21NO5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.1 M HEPES-Tris, 0.4 M sodium malonate, 26 % (w/v) PEG 3350, 8 % (v/v) glycerol, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 14, 2012
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→47 Å / Num. all: 30847 / Num. obs: 30847 / % possible obs: 99.9 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 84.4 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 19
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.7-2.90.4741.6199.7
2.9-30.2262.9199.9
3-3.20.1395.5199.8
3.2-3.50.0779.71100
3.5-3.80.05110.9199.9
3.8-4.30.03419.1199.9
4.3-4.90.02525.91100
4.9-60.02624.51100
6-8.50.02425.11100
8.5-470.01826.3199.3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.954 Å / SU ML: 0.34 / σ(F): 1.37 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1543 5 %
Rwork0.2047 --
obs0.2058 30842 99.87 %
all-30842 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5143 0 125 67 5335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015395
X-RAY DIFFRACTIONf_angle_d1.267291
X-RAY DIFFRACTIONf_dihedral_angle_d14.6641967
X-RAY DIFFRACTIONf_chiral_restr0.089802
X-RAY DIFFRACTIONf_plane_restr0.006929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78720.34341390.30992636X-RAY DIFFRACTION100
2.7872-2.88680.31161400.28872653X-RAY DIFFRACTION100
2.8868-3.00230.30561380.2732626X-RAY DIFFRACTION100
3.0023-3.13890.29011390.26712649X-RAY DIFFRACTION100
3.1389-3.30440.24721380.26012641X-RAY DIFFRACTION100
3.3044-3.51140.24081420.22832679X-RAY DIFFRACTION100
3.5114-3.78240.26611390.21472646X-RAY DIFFRACTION100
3.7824-4.16280.23411400.19842666X-RAY DIFFRACTION100
4.1628-4.76460.17281410.15892668X-RAY DIFFRACTION100
4.7646-6.0010.18441430.17332701X-RAY DIFFRACTION100
6.001-46.96090.22171440.19232734X-RAY DIFFRACTION100
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)
13.7044-3.37110.30597.444-1.29313.9172-0.0078-1.06940.16790.76670.3401-0.349-0.5220.2646-0.28680.7747-0.2999-0.10130.9453-0.06560.5973-17.645737.177238.3912
23.3435-0.0046-0.90344.25350.08084.56670.26040.07-0.20430.3136-0.38730.2895-0.1241-0.62870.13350.3155-0.07530.05120.5646-0.01540.4337-26.33224.516715.7043
33.4941-0.3457-1.3563.06360.14217.34340.0431-0.3355-0.22630.4278-0.2758-0.47710.5180.69380.15220.3625-0.086-0.07930.60870.11840.7506-10.378416.909816.9985
45.5092-5.09143.41834.2225-3.01241.73890.96411.69330.4478-0.8105-1.2311-0.6285-0.20260.33880.30680.85570.42360.22461.44560.24121.0346-24.809740.066-10.9787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 53:238)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 239:534)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 535:652)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 653:715)

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