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- EMDB-38227: C. elegans apo-SID1 structure -

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Basic information

Entry
Database: EMDB / ID: EMD-38227
TitleC. elegans apo-SID1 structure
Map data
Sample
  • Complex: dimer of sid1
    • Protein or peptide: Systemic RNA interference defective protein 1
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsdsRNA recognition / MEMBRANE 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 speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.21 Å
AuthorsGong DS
Funding support China, 1 items
OrganizationGrant numberCountry
Other government32271254 China
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Structural basis for double-stranded RNA recognition by SID1.
Authors: Runhao Wang / Ye Cong / Dandan Qian / Chuangye Yan / Deshun Gong /
Abstract: The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for ...The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for double-stranded (ds) RNA recognition by SID1 family remains elusive. Here, we report the cryo-EM structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA, both at a resolution of 2.2 Å. The dimeric cSID1 interacts with two dsRNA molecules simultaneously. The dsRNA is located at the interface between β-strand rich domain (BRD)1 and BRD2 and nearly parallel to the membrane plane. In addition to extensive ionic interactions between basic residues and phosphate backbone, several hydrogen bonds are formed between 2'-hydroxyl group of dsRNA and the contact residues. Additionally, the electrostatic potential surface shows three basic regions are fitted perfectly into three major grooves of dsRNA. These structural characteristics enable cSID1 to bind dsRNA in a sequence-independent manner and to distinguish between DNA and RNA. The cSID1 exhibits no conformational changes upon binding dsRNA, with the exception of a few binding surfaces. Structural mapping of dozens of loss-of-function mutations allows potential interpretation of their diverse functional mechanisms. Our study marks an important step toward mechanistic understanding of the SID1 family-mediated dsRNA uptake.
History
DepositionDec 7, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38227.png

Downloads & links

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Map

FileDownload / File: emd_38227.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.713
Minimum - Maximum-2.5400383 - 4.905752
Average (Standard dev.)-0.00021410648 (±0.12494379)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38227_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38227_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dimer of sid1

EntireName: dimer of sid1
Components
  • Complex: dimer of sid1
    • Protein or peptide: Systemic RNA interference defective protein 1
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: dimer of sid1

SupramoleculeName: dimer of sid1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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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: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 90.081664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIRVYLIILM HLVIGLTHHH HHHVEDYKDD DDKQNNSTTP SPIITSSNSS VLVFEISSKM KMIEKKLEAN TVHVLRLELD QSFILDLTK VAAEIVDSSK YSKEDGVILE VTVSNGRDSF LLKLPTVYPN LKLYTDGKLL NPLVEQDFGA HRKRHRIGDP H FHQNLIVT ...String:
MIRVYLIILM HLVIGLTHHH HHHVEDYKDD DDKQNNSTTP SPIITSSNSS VLVFEISSKM KMIEKKLEAN TVHVLRLELD QSFILDLTK VAAEIVDSSK YSKEDGVILE VTVSNGRDSF LLKLPTVYPN LKLYTDGKLL NPLVEQDFGA HRKRHRIGDP H FHQNLIVT VQSRLNADID YRLHVTHLDR AQYDFLKFKT GQTTKTLSNQ KLTFVKPIGF FLNCSEQNIS QFHVTLYSED DI CANLITV PANESIYDRS VISDKTHNRR VLSFTKRADI FFTETEISMF KSFRIFVFIA PDDSGCSTNT SRKSFNEKKK ISF EFKKLE NQSYAVPTAL MMIFLTTPCL LFLPIVINII KNSRKLAPSQ SNLISFSPVP SEQRDMDLSH DEQQNTSSEL ENNG EIPAA ENQIVEEITA ENQETSVEEG NREIQVKIPL KQDSLSLHGQ MLQYPVAIIL PVLMHTAIEF HKWTTSTMAN RDEMC FHNH ACARPLGELR AWNNIITNIG YTLYGAIFIV LSICRRGRHE YSHVFGTYEC TLLDVTIGVF MVLQSIASAT YHICPS DVA FQFDTPCIQV ICGLLMVRQW FVRHESPSPA YTNILLVGVV SLNFLISAFS KTSYVRFIIA VIHVIVVGSI CLAKERS LG SEKLKTRFFI MAFSMGNFAA IVMYLTLSAF HLNQIATYCF IINCIMYLMY YGCMKVLHSE RITSKAKLCG ALSLLAWA V AGFFFFQDDT DWTRSAAASR ALNKPCLLLG FFGSHDLWHI FGALAGLFTF IFVSFVDDDL INTRKTSINI F

UniProtKB: Systemic RNA interference defective protein 1

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Macromolecule #3: ZINC ION

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

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 8 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #5: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 5 / Number of copies: 2 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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: ETHANE

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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: 1.8 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 762464
FSC plot (resolution estimation)

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