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- PDB-3wsz: SorLA Vps10p domain in complex with Abeta-derived peptide -

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Basic information

Entry
Database: PDB / ID: 3wsz
TitleSorLA Vps10p domain in complex with Abeta-derived peptide
Components
  • 10-mer peptide
  • Sortilin-related receptor
KeywordsPROTEIN BINDING / Beta-Propeller / Receptor
Function / homology
Function and homology information


positive regulation of early endosome to recycling endosome transport / negative regulation of neurofibrillary tangle assembly / positive regulation of glial cell-derived neurotrophic factor production / perinucleolar compartment / positive regulation of endocytic recycling / Golgi cisterna / positive regulation of ER to Golgi vesicle-mediated transport / post-Golgi vesicle-mediated transport / adaptive thermogenesis / protein retention in Golgi apparatus ...positive regulation of early endosome to recycling endosome transport / negative regulation of neurofibrillary tangle assembly / positive regulation of glial cell-derived neurotrophic factor production / perinucleolar compartment / positive regulation of endocytic recycling / Golgi cisterna / positive regulation of ER to Golgi vesicle-mediated transport / post-Golgi vesicle-mediated transport / adaptive thermogenesis / protein retention in Golgi apparatus / low-density lipoprotein particle receptor activity / endosome to plasma membrane protein transport / negative regulation of triglyceride catabolic process / protein localization to Golgi apparatus / positive regulation of protein localization to early endosome / low-density lipoprotein particle binding / positive regulation of protein exit from endoplasmic reticulum / negative regulation of amyloid precursor protein catabolic process / protein targeting to lysosome / aspartic-type endopeptidase inhibitor activity / multivesicular body membrane / neuropeptide binding / regulation of smooth muscle cell migration / transport vesicle membrane / insulin receptor recycling / nuclear envelope lumen / diet induced thermogenesis / negative regulation of amyloid-beta formation / protein maturation / negative regulation of BMP signaling pathway / neuropeptide signaling pathway / protein targeting / negative regulation of protein-containing complex assembly / positive regulation of insulin receptor signaling pathway / positive regulation of adipose tissue development / multivesicular body / receptor-mediated endocytosis / trans-Golgi network / recycling endosome / small GTPase binding / negative regulation of neurogenesis / positive regulation of protein catabolic process / recycling endosome membrane / transmembrane signaling receptor activity / cell migration / amyloid-beta binding / early endosome membrane / early endosome / endosome membrane / endosome / Amyloid fiber formation / Golgi membrane / neuronal cell body / endoplasmic reticulum membrane / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain ...VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / EGF-like domain signature 2. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Sortilin-related receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsKitago, Y. / Nakata, Z. / Nagae, M. / Nogi, T. / Takagi, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structural basis for amyloidogenic peptide recognition by sorLA.
Authors: Kitago, Y. / Nagae, M. / Nakata, Z. / Yagi-Utsumi, M. / Takagi-Niidome, S. / Mihara, E. / Nogi, T. / Kato, K. / Takagi, J.
History
DepositionMar 30, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Derived calculations / Category: citation / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-related receptor
C: 10-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1826
Polymers77,2982
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint9 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.735, 163.735, 121.093
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Sortilin-related receptor / Neuronal extracellular receptor


Mass: 76568.766 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 86-753
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORL1 / Plasmid: pEF / Cell line (production host): CHO Cells / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): lec 3.2.8.1 / References: UniProt: Q92673
#2: Protein/peptide 10-mer peptide


Mass: 728.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human)
#3: 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.: 4
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
Sequence detailsTHIS RESIDUE BELONGS TO PROTEIN SEQUENCE, 29TH GLU OF Q92673.

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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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M Tris, 1.41M Sodium Acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2012
Details: The double crystal monochromator and the K-B mirror system
RadiationMonochromator: Double Si 111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 16303 / Num. obs: 16271 / % possible obs: 99.8 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 7.6 % / Biso Wilson estimate: 99.1 Å2 / Rsym value: 0.07 / Net I/σ(I): 29.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 4.77 / Num. unique all: 1580 / Rsym value: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
UGUISdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WSY

3wsy


Resolution: 3.201→49.009 Å / FOM work R set: 0.7513 / SU ML: 0.38 / σ(F): 1.35 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2963 816 5.02 %RANDOM
Rwork0.2729 ---
obs0.274 16244 99.7 %-
all-16293 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.77 Å2 / Biso mean: 129.93 Å2 / Biso min: 88.55 Å2
Refinement stepCycle: LAST / Resolution: 3.201→49.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4525 0 56 0 4581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064702
X-RAY DIFFRACTIONf_angle_d1.0496367
X-RAY DIFFRACTIONf_chiral_restr0.068689
X-RAY DIFFRACTIONf_plane_restr0.004812
X-RAY DIFFRACTIONf_dihedral_angle_d14.2791688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2015-3.4020.34771360.331425032639100
3.402-3.66460.3791410.323925122653100
3.6646-4.03320.33671570.30525092666100
4.0332-4.61650.29521260.263725622688100
4.6165-5.81480.25711320.247926112743100
5.8148-49.01490.26671240.25892731285599

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