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- EMDB-32117: Dimer structure of SORLA -

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Basic information

Entry
Database: EMDB / ID: EMD-32117
TitleDimer structure of SORLA
Map data
Sample
  • Complex: Dimer conformation of SORLA
    • Protein or peptide: Sortilin-related receptor
KeywordsProtein sorting receptor / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXi Z / Cang W / Chuang L
Funding support China, 1 items
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, 2021-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32117.png

Downloads & links

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Map

FileDownload / File: emd_32117.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 344.32 Å		1.08 Å/pix.
x 320 pix.
= 344.32 Å		1.08 Å/pix.
x 320 pix.
= 344.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.394
Minimum - Maximum-3.4945416 - 5.291032
Average (Standard dev.)0.00052577653 (±0.06614003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 344.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Dimer conformation of SORLA

EntireName: Dimer conformation of SORLA
Components
  • Complex: Dimer conformation of SORLA
    • Protein or peptide: Sortilin-related receptor

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Supramolecule #1: Dimer conformation of SORLA

SupramoleculeName: Dimer conformation of SORLA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sortilin-related receptor

MacromoleculeName: Sortilin-related receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.835891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PIKVYGQVSL NDSHNQMVVH WAGEKSNVIV ALARDSLALA RPKSSDVYVS YDYGKSFKKI SDKLNFGLGN RSEAVIAQFY HSPADNKRY IFADAYAQYL WITFDFCNTL QGFSIPFRAA DLLLHSKASN LLLGFDRSHP NKQLWKSDDF GQTWIMIQEH V KSFSWGID ...String:
PIKVYGQVSL NDSHNQMVVH WAGEKSNVIV ALARDSLALA RPKSSDVYVS YDYGKSFKKI SDKLNFGLGN RSEAVIAQFY HSPADNKRY IFADAYAQYL WITFDFCNTL QGFSIPFRAA DLLLHSKASN LLLGFDRSHP NKQLWKSDDF GQTWIMIQEH V KSFSWGID PYDKPNTIYI ERHEPSGYST VFRSTDFFQS RENQEVILEE VRDFQLRDKY MFATKVVHLL GSEQQSSVQL WV SFGRKPM RAAQFVTRHP INEYYIADAS EDQVFVCVSH SNNRTNLYIS EAEGLKFSLS LENVLYYSPG GAGSDTLVRY FAN EPFADF HRVEGLQGVY IATLINGSMN EENMRSVITF DKGGTWEFLQ APAFTGYGEK INCELSQGCS LHLAQRLSQL LNLQ LRRMP ILSKESAPGL IIATGSVGKN LASKTNVYIS SSAGARWREA LPGPHYYTWG DHGGIITAIA QGMETNELKY STNEG ETWK TFIFSEKPVF VYGLLTEPGE KSTVFTIFGS NKENVHSWLI LQVNATDALG VPCTENDYKL WSPSDERGNE CLLGHK TVF KRRTPHATCF NGEDFDRPVV VSNCSCTRED YECDFGFKMS EDLSLEVCVP DPEFSGKSYS PPVPCPVGST YRRTRGY RK ISGDTCSGGD VEARLEGELV PC

UniProtKB: Sortilin-related receptor

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: OTHER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 751415
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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