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- PDB-3f6k: Crystal structure of the Vps10p domain of human sortilin/NTS3 in ... -

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Basic information

Entry
Database: PDB / ID: 3f6k
TitleCrystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin
Components
  • Neurotensin
  • Sortilin
KeywordsSIGNALING PROTEIN / PROTEIN SORTING RECEPTOR / 10-bladed beta-propeller / Cys-rich domains / sSortilin / sortilin Vps10p-D / protein-peptide complex / Developmental protein / Differentiation / Endocytosis / Endoplasmic reticulum / Endosome / Glycoprotein / Golgi apparatus / Lysosome / Membrane / Phosphoprotein / Receptor / Transmembrane / Transport / Cytoplasmic vesicle / Secreted
Function / homology
Function and homology information


neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / myotube differentiation / neuropeptide receptor binding / 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 ...neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / myotube differentiation / neuropeptide receptor binding / 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 / neuropeptide hormone activity / 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 / axon terminus / clathrin-coated pit / transport vesicle / blood vessel diameter maintenance / Peptide ligand-binding receptors / ossification / response to insulin / endocytosis / positive regulation of NF-kappaB transcription factor activity / cytoplasmic vesicle / G alpha (q) signalling events / regulation of gene expression / nuclear membrane / lysosome / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / endosome membrane / G protein-coupled receptor signaling pathway / lysosomal membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular region / 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 / Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor ...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 / Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / 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
TRIETHYLENE GLYCOL / Neurotensin/neuromedin N / Sortilin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsQuistgaard, E.M. / Madsen, P. / Groftehauge, M.K. / Nissen, P. / Petersen, C.M. / Thirup, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Ligands bind to Sortilin in the tunnel of a ten-bladed beta-propeller domain.
Authors: Quistgaard, E.M. / Madsen, P. / Groftehauge, M.K. / Nissen, P. / Petersen, C.M. / Thirup, S.S.
History
DepositionNov 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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 3.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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
N: Neurotensin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7046
Polymers78,4512
Non-polymers1,2534
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-4.6 kcal/mol
Surface area30600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.760, 74.530, 108.330
Angle α, β, γ (deg.)90.00, 131.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1280-

HOH

DetailsTHE BIOLOGICAL UNIT IS A HETERODIMERIC COMPLEX OF THE PROTEIN MONOMER WITH THE PEPTIDE MONOMER.

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AN

#1: Protein Sortilin / Neurotensin receptor 3 / NTR3 / NTS3 / Glycoprotein 95 / Gp95 / 100 kDa NT receptor


Mass: 76774.703 Da / Num. of mol.: 1 / Fragment: UNP residues 78-756
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORT1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1 / References: UniProt: Q99523
#2: Protein/peptide Neurotensin /


Mass: 1675.948 Da / Num. of mol.: 1 / Fragment: UNP residues 151-163 / Source method: obtained synthetically
Details: Synthetic peptide purchased from Sigma. It represents the naturally occurring form of neurotensin in human, residues 151-163 of UniProt entry P30990, NEUT_HUMAN
References: UniProt: P30990

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Sugars , 2 types, 2 molecules

#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: 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, 307 molecules

#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsAUTHORS STATE THAT THE GLYCOSYLATIONS ARE COVALENTLY ATTACHED TO THE ASPARAGINES, THEREFORE THEY ...AUTHORS STATE THAT THE GLYCOSYLATIONS ARE COVALENTLY ATTACHED TO THE ASPARAGINES, THEREFORE THEY SHOULD NOT BE DESCRIBED AS SITE RECORDS. INSTEAD, WHAT SHOULD BE SHOWN IN SITE RECORDS, IS THE NEUROTENSIN BINDING SITE.
Sequence detailsIN VIVO, NEUROTENSIN (ENTITY 2) IS PRODUCED BY PROTEOLYTIC CLEAVAGE OF THE GENE PRODUCT, AND THE ...IN VIVO, NEUROTENSIN (ENTITY 2) IS PRODUCED BY PROTEOLYTIC CLEAVAGE OF THE GENE PRODUCT, AND THE RESULTING N-TERMINAL GLUTAMATE IS NATURALLY CONVERTED TO PYROGLUTAMATE.

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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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 19% PEG 6000, 600 mM NaCl, 3% Glycerol, 100 mM HEPES, 93 mM Tris-HCl, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95008 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 18, 2005
RadiationMonochromator: Fixed-exit LN2 cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95008 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 58793 / Num. obs: 56985 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 37.05 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.59
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.32 / Num. unique all: 7942 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2→40.32 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.61 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22879 2904 5.1 %RANDOM
Rwork0.20395 ---
all0.20524 56985 --
obs0.20524 56985 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.78 Å2
2--1.22 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 2→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 83 305 5600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225428
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.967357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0535658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68424.16250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7715890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0791528
X-RAY DIFFRACTIONr_chiral_restr0.1370.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024092
X-RAY DIFFRACTIONr_nbd_refined0.2380.22229
X-RAY DIFFRACTIONr_nbtor_refined0.3190.23763
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2680.2372
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.213
X-RAY DIFFRACTIONr_mcbond_it1.4461.53359
X-RAY DIFFRACTIONr_mcangle_it2.2925288
X-RAY DIFFRACTIONr_scbond_it3.27332370
X-RAY DIFFRACTIONr_scangle_it4.8164.52069
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 218 -
Rwork0.224 4048 -
obs--99.12 %
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)
12.1236-1.2281-0.3696.52720.67491.87620.0369-0.13080.20610.6073-0.0793-0.4944-0.08190.34810.04240.1094-0.0988-0.04130.15670.05240.090242.837669.777716.9772
21.0707-0.0319-0.07320.66140.12450.91610.0047-0.15250.10610.0768-0.0297-0.0546-0.12890.0460.0250.02-0.00260.00130.01790.0147-0.027220.646866.761821.8714
30.7834-1.4728-2.2283.49114.54056.5078-0.10390.0673-0.05320.2652-0.42270.44130.1682-0.64750.52660.15410.05150.02350.2974-0.11710.1577-11.165173.695623.9775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 155
2X-RAY DIFFRACTION2A156 - 629
3X-RAY DIFFRACTION3A630 - 716

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