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- PDB-8t8r: Sortilin-PGRN peptide complex -

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Basic information

Entry
Database: PDB / ID: 8t8r
TitleSortilin-PGRN peptide complex
Components
  • Paragranulin peptide
  • Sortilin
KeywordsTRANSPORT PROTEIN / Sortilin / Progranulin
Function / homology
Function and homology information


positive regulation of aspartic-type peptidase activity / positive regulation of inflammatory response to wounding / positive regulation of protein folding / neurotensin receptor activity, non-G protein-coupled / microglial cell activation involved in immune response / Golgi to lysosome transport / trophectodermal cell proliferation / positive regulation of trophectodermal cell proliferation / plasma membrane to endosome transport / positive regulation of defense response to bacterium ...positive regulation of aspartic-type peptidase activity / positive regulation of inflammatory response to wounding / positive regulation of protein folding / neurotensin receptor activity, non-G protein-coupled / microglial cell activation involved in immune response / Golgi to lysosome transport / trophectodermal cell proliferation / positive regulation of trophectodermal cell proliferation / plasma membrane to endosome transport / positive regulation of defense response to bacterium / negative regulation of microglial cell activation / myotube differentiation / positive regulation of lysosome organization / nerve growth factor receptor activity / Golgi to endosome transport / cerebellar climbing fiber to Purkinje cell synapse / maintenance of synapse structure / retromer complex binding / endosome transport via multivesicular body sorting pathway / nerve growth factor binding / vesicle organization / lysosomal protein catabolic process / lysosomal lumen acidification / positive regulation of axon regeneration / blastocyst hatching / protein targeting to lysosome / trans-Golgi network transport vesicle / negative regulation of neutrophil activation / astrocyte activation involved in immune response / clathrin-coated vesicle / lysosomal transport / lysosome organization / Golgi cisterna membrane / endosome to lysosome transport / Golgi Associated Vesicle Biogenesis / negative regulation of fat cell differentiation / neurotrophin TRK receptor signaling pathway / D-glucose import / locomotory exploration behavior / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of respiratory burst involved in inflammatory response / neuropeptide signaling pathway / clathrin-coated pit / embryo implantation / positive regulation of endothelial cell migration / ossification / epithelial cell proliferation / positive regulation of epithelial cell proliferation / cytokine activity / growth factor activity / trans-Golgi network / response to insulin / endocytosis / positive regulation of angiogenesis / azurophil granule lumen / late endosome / positive regulation of neuron apoptotic process / regulation of gene expression / protein-folding chaperone binding / retina development in camera-type eye / regulation of inflammatory response / cytoplasmic vesicle / nuclear membrane / negative regulation of neuron apoptotic process / early endosome / endosome membrane / lysosome / endosome / protein stabilization / positive regulation of cell migration / G protein-coupled receptor signaling pathway / lysosomal membrane / endoplasmic reticulum membrane / Neutrophil degranulation / perinuclear region of cytoplasm / enzyme binding / cell surface / endoplasmic reticulum / Golgi apparatus / signal transduction / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Granulins signature. / Granulin family / Granulin / Granulin superfamily / Granulin / Granulin / VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / : ...Granulins signature. / Granulin family / Granulin / Granulin superfamily / Granulin / Granulin / 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
Progranulin / Sortilin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsSrivastava, D.B. / Srivastava, A. / Cherf, G.M. / Low, L.Y. / Kannan, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structural studies of Sortilin-PGRN peptide complex
Authors: Srivastava, D.B. / Cherf, G.M. / Low, L.Y. / Kannan, G.
History
DepositionJun 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortilin
B: Paragranulin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3316
Polymers77,7162
Non-polymers1,6164
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint19 kcal/mol
Surface area32480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.945, 78.618, 111.200
Angle α, β, γ (deg.)90.00, 126.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 75826.672 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): HEK / Production host: Homo sapiens (human) / References: UniProt: Q99523
#2: Protein/peptide Paragranulin peptide


Mass: 1889.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P28799
#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-ROHGlycam 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
[][D-1-deoxy-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / 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
Has ligand of interestN
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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20.00 %w/ PEG 3350, 0.20 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99993 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 2.87→89.04 Å / Num. obs: 25644 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 19.36
Reflection shellResolution: 2.87→3.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.43 / Num. unique obs: 5633 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.87→44.56 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.92 / SU B: 23.899 / SU ML: 0.405 / Cross valid method: THROUGHOUT / ESU R: 0.778 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2867 682 2.7 %RANDOM
Rwork0.25803 ---
obs0.25877 24962 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 119.842 Å2
Baniso -1Baniso -2Baniso -3
1--7.95 Å2-0 Å21.48 Å2
2--5.6 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.87→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 106 0 5316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0115200
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164543
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.6637100
X-RAY DIFFRACTIONr_angle_other_deg0.4811.57410424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.001517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.110644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0590.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021175
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.65712.9672642
X-RAY DIFFRACTIONr_mcbond_other1.65712.9672642
X-RAY DIFFRACTIONr_mcangle_it3.0223.4263292
X-RAY DIFFRACTIONr_mcangle_other3.01923.4253293
X-RAY DIFFRACTIONr_scbond_it1.34813.1022558
X-RAY DIFFRACTIONr_scbond_other1.34813.1042559
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.50824.1993809
X-RAY DIFFRACTIONr_long_range_B_refined6.642155.119923
X-RAY DIFFRACTIONr_long_range_B_other6.642155.119924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.87→2.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 46 -
Rwork0.453 1791 -
obs--98.6 %

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