[English] 日本語
Yorodumi
- EMDB-36008: SIDT1 protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36008
TitleSIDT1 protein
Map data
Sample
  • Complex: T1
    • Protein or peptide: Green fluorescent protein,SID1 transmembrane family member 1
  • Ligand: CHOLESTEROL
  • Ligand: ZINC ION
  • Ligand: SODIUM IONSodium
  • Ligand: OLEIC ACID
  • Ligand: water
Keywordstransport T1 / TRANSCRIPTION
Function / homology
Function and homology information


RNA transmembrane transporter activity / RNA transport / cholesterol binding / bioluminescence / generation of precursor metabolites and energy / double-stranded RNA binding / lysosome / plasma membrane
Similarity search - Function
SID1 transmembrane family / dsRNA-gated channel SID-1 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / SID1 transmembrane family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsZhang JT / Jiang DH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural insights into double-stranded RNA recognition and transport by SID-1.
Authors: Jiangtao Zhang / Chunhua Zhan / Junping Fan / Dian Wu / Ruixue Zhang / Di Wu / Xinyao Chen / Ying Lu / Ming Li / Min Lin / Jianke Gong / Daohua Jiang /
Abstract: RNA uptake by cells is critical for RNA-mediated gene interference (RNAi) and RNA-based therapeutics. In Caenorhabditis elegans, RNAi is systemic as a result of SID-1-mediated double-stranded RNA ...RNA uptake by cells is critical for RNA-mediated gene interference (RNAi) and RNA-based therapeutics. In Caenorhabditis elegans, RNAi is systemic as a result of SID-1-mediated double-stranded RNA (dsRNA) across cells. Despite the functional importance, the underlying mechanisms of dsRNA internalization by SID-1 remain elusive. Here we describe cryogenic electron microscopy structures of SID-1, SID-1-dsRNA complex and human SID-1 homologs SIDT1 and SIDT2, elucidating the structural basis of dsRNA recognition and import by SID-1. The homodimeric SID-1 homologs share conserved architecture, but only SID-1 possesses the molecular determinants within its extracellular domains for distinguishing dsRNA from single-stranded RNA and DNA. We show that the removal of the long intracellular loop between transmembrane helix 1 and 2 attenuates dsRNA uptake and systemic RNAi in vivo, suggesting a possible endocytic mechanism of SID-1-mediated dsRNA internalization. Our study provides mechanistic insights into dsRNA internalization by SID-1, which may facilitate the development of dsRNA applications based on SID-1.
History
DepositionApr 26, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36008.png

Downloads & links

-
Map

FileDownload / File: emd_36008.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.962
Minimum - Maximum-5.8567076 - 7.8995166
Average (Standard dev.)0.00016368415 (±0.1532391)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_36008_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_36008_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : T1

EntireName: T1
Components
  • Complex: T1
    • Protein or peptide: Green fluorescent protein,SID1 transmembrane family member 1
  • Ligand: CHOLESTEROL
  • Ligand: ZINC ION
  • Ligand: SODIUM IONSodium
  • Ligand: OLEIC ACID
  • Ligand: water

-
Supramolecule #1: T1

SupramoleculeName: T1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Green fluorescent protein,SID1 transmembrane family member 1

MacromoleculeName: Green fluorescent protein,SID1 transmembrane family member 1
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 124.044672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS WSHPQFEKGG GSGGGSGGSA WSHPQFEKSK GEELFTGVVP ILVELDGDVN GHKFSVRGEG EGDATNGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKRHD FFKSAMPEGY VQERTISFKD DGTYKTRAEV K FEGDTLVN ...String:
MYRMQLLSCI ALSLALVTNS WSHPQFEKGG GSGGGSGGSA WSHPQFEKSK GEELFTGVVP ILVELDGDVN GHKFSVRGEG EGDATNGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKRHD FFKSAMPEGY VQERTISFKD DGTYKTRAEV K FEGDTLVN RIELKGIDFK EDGNILGHKL EYNFNSHNVY ITADKQKNGI KANFKIRHNV EDGSVQLADH YQQNTPIGDG PV LLPDNHY LSTQSVLSKD PNEKRDHMVL LEFVTAAGIT HGMDELEVLF QGPASPGHPA KSPRQPPAPR RDPFDAARGA DFD HVYSGV VNLSTENIYS FNYTSQPDQV TAVRVYVNSS SENLNYPVLV VVRQQKEVLS WQVPLLFQGL YQRSYNYQEV SRTL CPSEA TNETGPLQQL IFVDVASMAP LGAQYKLLVT KLKHFQLRTN VAFHFTASPS QPQYFLYKFP KDVDSVIIKV VSEMA YPCS VVSVQNIMCP VYDLDHNVEF NGVYQSMTKK AAITLQKKDF PGEQFFVVFV IKPEDYACGG SFFIQEKENQ TWNLQR KKN LEVTIVPSIK ESVYVKSSLF SVFIFLSFYL GCLLVGFVHY LRFQRKSIDG SFGSNDGSGN MVASHPIAAS TPEGSNY GT IDESSSSPGR QMSSSDGGPP GQSDTDSSVE ESDFDTMPDI ESDKNIIRTK MFLYLSDLSR KDRRIVSKKY KIYFWNII T IAVFYALPVI QLVITYQTVV NVTGNQDICY YNFLCAHPLG VLSAFNNILS NLGHVLLGFL FLLIVLRRDI LHRRALEAK DIFAVEYGIP KHFGLFYAMG IALMMEGVLS ACYHVCPNYS NFQFDTSFMY MIAGLCMLKL YQTRHPDINA SAYSAYASFA VVIMVTVLG VVFGKNDVWF WVIFSAIHVL ASLALSTQIY YMGRFKIDLG IFRRAAMVFY TDCIQQCSRP LYMDRMVLLV V GNLVNWSF ALFGLIYRPR DFASYMLGIF ICNLLLYLAF YIIMKLRSSE KVLPVPLFCI VATAVMWAAA LYFFFQNLSS WE GTPAESR EKNRECILLD FFDDHDIWHF LSATALFFSF LVLLTLDDDL DVVRRDQIPV F

UniProtKB: Green fluorescent protein, SID1 transmembrane family member 1

-
Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 8 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #5: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 5 / Number of copies: 2 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID / Oleic acid

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145765

+
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