[English] 日本語
Yorodumi
- EMDB-32117: Dimer structure of SORLA -

+
Open data


ID or keywords:

Loading...

-
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 / adaptive thermogenesis / post-Golgi vesicle-mediated transport / 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 / adaptive thermogenesis / post-Golgi vesicle-mediated transport / protein retention in Golgi apparatus / protein transporter 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 / 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 / nuclear envelope lumen / diet induced thermogenesis / negative regulation of amyloid-beta formation / negative regulation of BMP signaling pathway / neuropeptide signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of insulin receptor signaling pathway / protein targeting / positive regulation of adipose tissue development / multivesicular body / receptor-mediated endocytosis / trans-Golgi network / recycling endosome / small GTPase binding / negative regulation of neurogenesis / 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 / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol
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 / 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
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

-
Structure visualization

Supplemental images

emd_32117.png

Downloads & links

-
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 °

-
Supplemental data

-
Sample components

-
Entire : Dimer conformation of SORLA

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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: OTHER

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more