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- EMDB-34850: dsRNA transporter -

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Basic information

Entry
Database: EMDB / ID: EMD-34850
TitledsRNA transporter
Map data
Sample
  • Complex: dsRNA transporter
    • Protein or peptide: Systemic RNA interference defective protein 1
    • RNA: RNA (37-MER)
    • RNA: RNA (37-MER)
  • Ligand: ZINC ION
KeywordsdsRNA transporter / RNA BINDING PROTEIN
Function / homology
Function and homology information


RNA transmembrane transporter activity / dsRNA transport / RNA transport / regulatory ncRNA-mediated post-transcriptional gene silencing / double-stranded RNA binding / lysosome / membrane / plasma membrane
Similarity search - Function
SID1 transmembrane family / dsRNA-gated channel SID-1
Similarity search - Domain/homology
Systemic RNA interference defective protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsJiang DH / Zhang JT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271272 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
DepositionNov 25, 2022-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34850.png

Downloads & links

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Map

FileDownload / File: emd_34850.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.304
Minimum - Maximum-1.4690503 - 2.1334658
Average (Standard dev.)0.0021298819 (±0.058546253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34850_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34850_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : dsRNA transporter

EntireName: dsRNA transporter
Components
  • Complex: dsRNA transporter
    • Protein or peptide: Systemic RNA interference defective protein 1
    • RNA: RNA (37-MER)
    • RNA: RNA (37-MER)
  • Ligand: ZINC ION

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Supramolecule #1: dsRNA transporter

SupramoleculeName: dsRNA transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Systemic RNA interference defective protein 1

MacromoleculeName: Systemic RNA interference defective protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.02757 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIRVYLIILM HLVIGLTQNN STTPSPIITS SNSSVLVFEI SSKMKMIEKK LEANTVHVLR LELDQSFILD LTKVAAEIVD SSKYSKEDG VILEVTVSNG RDSFLLKLPT VYPNLKLYTD GKLLNPLVEQ DFGAHRKRHR IGDPHFHQNL IVTVQSRLNA D IDYRLHVT ...String:
MIRVYLIILM HLVIGLTQNN STTPSPIITS SNSSVLVFEI SSKMKMIEKK LEANTVHVLR LELDQSFILD LTKVAAEIVD SSKYSKEDG VILEVTVSNG RDSFLLKLPT VYPNLKLYTD GKLLNPLVEQ DFGAHRKRHR IGDPHFHQNL IVTVQSRLNA D IDYRLHVT HLDRAQYDFL KFKTGQTTKT LSNQKLTFVK PIGFFLNCSE QNISQFHVTL YSEDDICANL ITVPANESIY DR SVISDKT HNRRVLSFTK RADIFFTETE ISMFKSFRIF VFIAPDDSGC STNTSRKSFN EKKKISFEFK KLENQSYAVP TAL MMIFLT TPCLLFLPIV INIIKNSRKL APSQSNLISF SPVPSEQRDM DLSHDEQQNT SSELENNGEI PAAENQIVEE ITAE NQETS VEEGNREIQV KIPLKQDSLS LHGQMLQYPV AIILPVLMHT AIEFHKWTTS TMANRDEMCF HNHACARPLG ELRAW NNII TNIGYTLYGA IFIVLSICRR GRHEYSHVFG TYECTLLDVT IGVFMVLQSI ASATYHICPS DVAFQFDTPC IQVICG LLM VRQWFVRHES PSPAYTNILL VGVVSLNFLI SAFSKTSYVR FIIAVIHVIV VGSICLAKER SLGSEKLKTR FFIMAFS MG NFAAIVMYLT LSAFHLNQIA TYCFIINCIM YLMYYGCMKV LHSERITSKA KLCGALSLLA WAVAGFFFFQ DDTDWTRS A AASRALNKPC LLLGFFGSHD LWHIFGALAG LFTFIFVSFV DDDLINTRKT SINIF

UniProtKB: Systemic RNA interference defective protein 1

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Macromolecule #2: RNA (37-MER)

MacromoleculeName: RNA (37-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.894137 KDa
SequenceString:
GGGCAAUGUG ACUGCAUCAG CAGUCACAUU GCCCAAG

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Macromolecule #3: RNA (37-MER)

MacromoleculeName: RNA (37-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.825017 KDa
SequenceString:
CUUGGGCAAU GUGACUGCUG AUGCAGUCAC AUUGCCC

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108090
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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