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- PDB-3wsx: SorLA Vps10p domain in ligand-free form -

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Basic information

Entry
Database: PDB / ID: 3wsx
TitleSorLA Vps10p domain in ligand-free form
ComponentsSortilin-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 / adaptive thermogenesis / protein retention in Golgi apparatus / post-Golgi vesicle-mediated transport ...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 / adaptive thermogenesis / protein retention in Golgi apparatus / post-Golgi vesicle-mediated transport / protein transporter activity / negative regulation of triglyceride catabolic process / positive regulation of protein exit from endoplasmic reticulum / protein localization to Golgi apparatus / positive regulation of protein localization to early endosome / low-density lipoprotein particle receptor activity / negative regulation of amyloid precursor protein catabolic process / endosome to plasma membrane protein transport / low-density lipoprotein particle binding / aspartic-type endopeptidase inhibitor activity / protein targeting to lysosome / multivesicular body membrane / regulation of smooth muscle cell migration / neuropeptide binding / retrograde transport, endosome to Golgi / insulin receptor recycling / transport vesicle membrane / diet induced thermogenesis / nuclear envelope lumen / negative regulation of amyloid-beta formation / negative regulation of BMP signaling pathway / positive regulation of insulin receptor signaling pathway / neuropeptide signaling pathway / protein targeting / negative regulation of protein-containing complex assembly / positive regulation of adipose tissue development / multivesicular body / receptor-mediated endocytosis / trans-Golgi network / recycling endosome / negative regulation of neurogenesis / small GTPase binding / recycling endosome membrane / positive regulation of protein catabolic process / transmembrane signaling receptor activity / cell migration / amyloid-beta binding / early endosome membrane / early endosome / endosome / endosome membrane / Amyloid fiber formation / Golgi membrane / neuronal cell body / endoplasmic reticulum membrane / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
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 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. ...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 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 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 / Fibronectin type III domain / EGF-like domain signature 2. / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Sortilin-related receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortilin-related receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,25614
Polymers82,8401
Non-polymers1,41613
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.371, 126.371, 290.282
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 82839.961 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 29-753
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: 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.: 3
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
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
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: 4.04 Å3/Da / Density % sol: 69.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Sodium Acetate, 1.2M Sodium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 270 / Detector: CCD / Date: Mar 8, 2010
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: 2.35→50 Å / Num. all: 57640 / Num. obs: 56199 / % possible obs: 97.5 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 11.4 % / Biso Wilson estimate: 56.6 Å2 / Rsym value: 0.057 / Net I/σ(I): 34
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.37 / Num. unique all: 5658 / Rsym value: 0.486 / % possible all: 98.7

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Processing

Software
NameVersionClassification
UGUISdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F6K

3f6k


Resolution: 2.35→47.63 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.525 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): -1 / ESU R: 0.196 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23757 2849 5.1 %RANDOM
Rwork0.20759 ---
obs0.20912 53349 97.6 %-
all-54661 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.109 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 86 150 5066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195037
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9496812
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7623.745243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02215798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5491529
X-RAY DIFFRACTIONr_chiral_restr0.1060.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213849
X-RAY DIFFRACTIONr_gen_planes_other
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
LS refinement shellResolution: 2.354→2.415 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 195 -
Rwork0.318 3910 -
obs--98.87 %

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