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- PDB-4po7: Structure of the Sortilin:neurotensin complex at excess neurotens... -

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Basic information

Entry
Database: PDB / ID: 4po7
TitleStructure of the Sortilin:neurotensin complex at excess neurotensin concentration
Components
  • Neurotensin/neuromedin N
  • Sortilin
KeywordsPROTEIN BINDING / 10 bladed beta-propeller / PROTEIN SORTING RECEPTOR / Neurotensin / Glycosylation / Trans Golgi Network
Function / homology
Function and homology information


neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / neuropeptide receptor binding / 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 ...neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / neuropeptide receptor binding / 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 / 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 / ossification / Peptide ligand-binding receptors / 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 / Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 ...Sortilin Vps10-D, 10CC-a domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #270 / Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / 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
Neurotensin/neuromedin N / Sortilin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsQuistgaard, E.M. / Groftehauge, M.K. / Thirup, S.S.
CitationJournal: Protein Sci. / Year: 2014
Title: Revisiting the structure of the Vps10 domain of human sortilin and its interaction with neurotensin.
Authors: Quistgaard, E.M. / Grftehauge, M.K. / Madsen, P. / Pallesen, L.T. / Christensen, B. / Srensen, E.S. / Nissen, P. / Petersen, C.M. / Thirup, S.S.
History
DepositionFeb 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Other
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _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 / 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 / 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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_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 / _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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 21, 2020Group: Data collection / Structure summary / Category: chem_comp / reflns_shell / Item: _chem_comp.pdbx_synonyms / _reflns_shell.Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortilin
N: Neurotensin/neuromedin N
P: Neurotensin/neuromedin N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7157
Polymers80,1273
Non-polymers1,5894
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.010, 78.650, 110.980
Angle α, β, γ (deg.)90.00, 126.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ANP

#1: Protein Sortilin / 100 kDa NT receptor / Glycoprotein 95 / Gp95 / Neurotensin receptor 3 / NT3 / NTR3


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 / Cell line (production host): CHO-K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q99523
#2: Protein/peptide Neurotensin/neuromedin N / Large neuromedin N / NmN-125 / Neuromedin N / NN / NmN / Neurotensin / NT / Tail peptide


Mass: 1675.948 Da / Num. of mol.: 2 / Fragment: unp residues 151-163 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P30990

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Sugars , 2 types, 3 molecules

#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.: 2
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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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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Non-polymers , 2 types, 109 molecules

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


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.54 Å3/Da / Density % sol: 65.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 20% PEG 6k, 300 mM sodium malonate, 3% glycerol and 100 mM TrisHCl, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.90736 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90736 Å / Relative weight: 1
ReflectionResolution: 2.66→20.97 Å / Num. all: 32509 / Num. obs: 32040 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 71.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.79
Reflection shellResolution: 2.66→2.73 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.1 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.3_1479) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→20.968 Å / SU ML: 0.31 / σ(F): 1.36 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 1620 5.06 %
Rwork0.1661 --
obs0.1684 31988 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→20.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5305 0 105 108 5518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045548
X-RAY DIFFRACTIONf_angle_d0.7567508
X-RAY DIFFRACTIONf_dihedral_angle_d12.2082009
X-RAY DIFFRACTIONf_chiral_restr0.031835
X-RAY DIFFRACTIONf_plane_restr0.003953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.73810.28611310.24162499X-RAY DIFFRACTION99
2.7381-2.82630.33441320.24852500X-RAY DIFFRACTION99
2.8263-2.92710.29041130.24112554X-RAY DIFFRACTION99
2.9271-3.04390.3031430.22252502X-RAY DIFFRACTION99
3.0439-3.1820.27711380.21092540X-RAY DIFFRACTION99
3.182-3.34910.25611530.19992489X-RAY DIFFRACTION99
3.3491-3.5580.25881330.17892538X-RAY DIFFRACTION100
3.558-3.83120.2061410.16932524X-RAY DIFFRACTION99
3.8312-4.21390.21221380.14492565X-RAY DIFFRACTION100
4.2139-4.81720.16021350.12742543X-RAY DIFFRACTION99
4.8172-6.0450.16351340.14162579X-RAY DIFFRACTION100
6.045-20.96880.19441290.15872535X-RAY DIFFRACTION96
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)
13.8101-1.9952-0.26558.6691-0.60541.0346-0.3265-1.0704-0.61420.62190.15010.14210.43350.4570.1450.8528-0.0821-0.2161.15990.26880.6391-12.8992-10.765841.0406
29.2328-5.6548-2.04665.06791.72581.6789-0.1941-1.1508-0.41420.7250.32250.2594-0.3320.7003-0.09571.0668-0.1331-0.13640.98890.10180.53-21.03834.398449.0542
37.6992-2.1466-0.07593.8265-1.61563.64220.0656-0.68290.13040.57370.2301-0.4786-0.94620.2535-0.2381.0365-0.2867-0.04840.7712-0.05770.6005-17.164715.399738.7501
42.0832-0.14280.62594.33092.568560.21460.19590.4843-0.1999-0.19430.0045-1.4986-0.170.01630.84250.04830.11890.5140.1080.5468-26.530917.523415.6405
55.4614-0.1584-1.62746.5693-1.05825.01630.02520.3507-0.3781-0.0356-0.20880.14960.1855-0.44450.11590.2867-0.01490.00650.5138-0.0740.4152-27.966-12.402113.1552
63.06130.0096-0.67262.06260.3184.64450.021-0.5136-0.46380.481-0.2073-0.5930.60650.74770.17820.56050.0316-0.10460.64770.20450.729-12.1186-16.781526.1538
75.3921-7.87353.27067.311-4.76631.45560.59951.56860.8871-0.7645-1.1992-0.9263-0.02940.51330.44470.78710.27320.11811.46120.25891.0291-22.54817.5846-9.6565
85.5103-2.85273.96685.8794-1.34523.03210.69881.0507-1.04632.5242-1.3427-0.1027-1.57512.18480.16791.1643-0.146-0.19011.0911-0.07580.704-26.38752.155127.8553
99.4509-7.7308-0.46058.24220.46481.6172-0.78970.02041.1561-0.30010.0859-0.85360.548-1.26890.96241.5314-0.1106-0.43261.70080.35311.0833-27.590421.61250.5864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 96)
2X-RAY DIFFRACTION2chain 'A' and ((resid 97 through 137 ) or (resid 807))
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 193 )
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 352 )
5X-RAY DIFFRACTION5chain 'A' and ((resid 353 through 470 ) or (resid 801 through 803))
6X-RAY DIFFRACTION6chain 'A' and ((resid 471 through 627 ) or (resid 804 through 806))
7X-RAY DIFFRACTION7chain 'A' and (resid 628 through 714 )
8X-RAY DIFFRACTION8chain 'N' and (resid 1 through 13 )
9X-RAY DIFFRACTION9chain 'P' and (resid 9 through 13 )

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