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- PDB-7vt0: Dimer structure of SORLA -

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Basic information

Entry
Database: PDB / ID: 7vt0
TitleDimer structure of SORLA
ComponentsSortilin-related receptor
KeywordsMEMBRANE PROTEIN / Protein sorting 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 / negative regulation of triglyceride catabolic process / protein localization to Golgi apparatus / positive regulation of protein localization to early endosome / positive regulation of protein exit from endoplasmic reticulum / endosome to plasma membrane protein transport / negative regulation of amyloid precursor protein catabolic process / low-density lipoprotein particle binding / protein targeting to lysosome / aspartic-type endopeptidase inhibitor activity / multivesicular body membrane / regulation of smooth muscle cell migration / neuropeptide binding / insulin receptor recycling / transport vesicle membrane / nuclear envelope lumen / diet induced thermogenesis / negative regulation of amyloid-beta formation / protein maturation / neuropeptide signaling pathway / negative regulation of BMP 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 / 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 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 ...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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXi, Z. / Cang, W. / Chuang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900868 China
CitationJournal: Biochem Biophys Res Commun / Year: 2022
Title: Cryo-EM structures reveal distinct apo conformations of sortilin-related receptor SORLA.
Authors: Xi Zhang / Cang Wu / Zhihong Song / Dayong Sun / Liting Zhai / Chuang Liu /
Abstract: Sorting-related receptor with A-type repeats (SORLA) is an important receptor for regulating normal cellular functions via protein sorting. Here, we determined the structures of the full-length SORLA ...Sorting-related receptor with A-type repeats (SORLA) is an important receptor for regulating normal cellular functions via protein sorting. Here, we determined the structures of the full-length SORLA and identified two distinct conformations of apo-SORLA using single-particle cryogenic electron microscopy. In contrast to homologous proteins, both monomer and dimer forms of SORLA existed in a neutral solution. Only three hydrogen bonds in the vicinity of the dimer interface implied the involvement in dimerization. The orientation of residue R490 was a key point for ligand binding. These results suggest a unique mechanism of SORLA dimerization for protein trafficking.
History
DepositionOct 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortilin-related receptor
B: Sortilin-related receptor


Theoretical massNumber of molelcules
Total (without water)149,6722
Polymers149,6722
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sortilin-related receptor / Low-density lipoprotein receptor relative with 11 ligand-binding repeats / LDLR relative with 11 ...Low-density lipoprotein receptor relative with 11 ligand-binding repeats / LDLR relative with 11 ligand-binding repeats / LR11 / SorLA-1 / Sorting protein-related receptor containing LDLR class A repeats / SorLA


Mass: 74835.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORL1, C11orf32 / Production host: Homo sapiens (human) / References: UniProt: Q92673
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dimer conformation of SORLA / Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 751415 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310809
ELECTRON MICROSCOPYf_angle_d0.71514653
ELECTRON MICROSCOPYf_dihedral_angle_d5.5261449
ELECTRON MICROSCOPYf_chiral_restr0.0451554
ELECTRON MICROSCOPYf_plane_restr0.0061909

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