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- PDB-8t8s: Sortilin-PGRN peptide complex -

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Basic information

Entry
Database: PDB / ID: 8t8s
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 / negative regulation of neutrophil activation / positive regulation of protein folding / neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / microglial cell activation involved in immune response / Golgi to lysosome transport / positive regulation of lysosome organization / myotube differentiation ...positive regulation of aspartic-type peptidase activity / positive regulation of inflammatory response to wounding / negative regulation of neutrophil activation / positive regulation of protein folding / neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / microglial cell activation involved in immune response / Golgi to lysosome transport / positive regulation of lysosome organization / myotube differentiation / cerebellar climbing fiber to Purkinje cell synapse / positive regulation of defense response to bacterium / negative regulation of microglial cell activation / plasma membrane to endosome transport / maintenance of synapse structure / retromer complex binding / Golgi to endosome transport / nerve growth factor receptor activity / vesicle organization / endosome transport via multivesicular body sorting pathway / lysosomal lumen acidification / nerve growth factor binding / protein targeting to lysosome / trans-Golgi network transport vesicle / astrocyte activation involved in immune response / clathrin-coated vesicle / lysosomal transport / Golgi cisterna membrane / Golgi Associated Vesicle Biogenesis / lysosome organization / negative regulation of fat cell differentiation / endosome to lysosome transport / positive regulation of axon regeneration / glucose import / neurotrophin TRK receptor signaling pathway / negative regulation of respiratory burst involved in inflammatory response / extrinsic apoptotic signaling pathway via death domain receptors / neuropeptide signaling pathway / clathrin-coated pit / positive regulation of endothelial cell migration / ossification / cytokine activity / positive regulation of epithelial cell proliferation / growth factor activity / response to insulin / trans-Golgi network / endocytosis / positive regulation of angiogenesis / azurophil granule lumen / positive regulation of neuron apoptotic process / late endosome / protein-folding chaperone binding / regulation of inflammatory response / cytoplasmic vesicle / regulation of gene expression / nuclear membrane / negative regulation of neuron apoptotic process / lysosome / early endosome / protein stabilization / endosome membrane / endosome / positive regulation of cell migration / G protein-coupled receptor signaling pathway / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / endoplasmic reticulum / signal transduction / RNA binding / extracellular space / 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 / Sortilin, neurotensin receptor 3, C-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: 2.99 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortilin
B: Sortilin
C: Paragranulin peptide
D: Paragranulin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,16812
Polymers155,4944
Non-polymers2,6748
Water32418
1
A: Sortilin
C: Paragranulin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2127
Polymers77,7472
Non-polymers1,4655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-7 kcal/mol
Surface area30480 Å2
MethodPISA
2
B: Sortilin
D: Paragranulin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9555
Polymers77,7472
Non-polymers1,2093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-6 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)237.030, 237.030, 89.427
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 75826.672 Da / Num. of mol.: 2
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: 1920.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P28799

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Sugars , 2 types, 5 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.: 4
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.: 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, 21 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.88 Å3/Da / Density % sol: 74.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.10 M Tris, 30.00 %w/v PEG 3000, 0.20 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999982608809 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999982608809 Å / Relative weight: 1
ReflectionResolution: 2.99→205.27 Å / Num. obs: 58113 / % possible obs: 99.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.87
Reflection shellResolution: 2.99→3.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.45 / Num. unique obs: 12291 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.99→205.27 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.873 / SU B: 19.182 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.573 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.275 504 0.9 %RANDOM
Rwork0.234 ---
obs0.234 57607 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.54 Å20 Å2
2--1.07 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 2.99→205.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10491 0 173 18 10682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910729
X-RAY DIFFRACTIONr_bond_other_d0.0020.029650
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.95914617
X-RAY DIFFRACTIONr_angle_other_deg1.186322196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78551328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80824.022465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.728151619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3781550
X-RAY DIFFRACTIONr_chiral_restr0.0850.21652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212140
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022492
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A374100.08
12B374100.08
21C6320.13
22D6320.13
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 38 -
Rwork0.373 4197 -
obs--98.24 %

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