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- EMDB-62886: Structure of SID-1 in complex with dsRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-62886
TitleStructure of SID-1 in complex with dsRNA
Map data
Sample
  • Complex: SID-1 in complex with dsRNA
    • Protein or peptide: Systemic RNA interference defective protein 1
    • RNA: RNA (24-mer)
    • RNA: RNA (24-mer)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
KeywordsdsRNA / Membrane protein / Complex / MEMBRANE PROTEIN-RNA complex
Function / homology
Function and homology information


dsRNA transport / RNA transmembrane transporter activity / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKumazaki K / Kusakizako T / Nishizawa T / Nureki O
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H05037 Japan
Japan Science and TechnologyJPMJCR20E2 Japan
Japan Agency for Medical Research and Development (AMED)JP19am01011115 Japan
CitationJournal: To Be Published
Title: Structural insights into SID1-mediated dsRNA uptake: A self-organizing endocytic mechanism
Authors: Takai A / Kumazaki K / Awazu T / Kambara T / Murakoshi S / Kato T / Hiraizumi M / Kise Y / Kusakizako T / Nishizawa T / Okada T / Nureki O
History
DepositionDec 27, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62886.png

Downloads & links

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Map

FileDownload / File: emd_62886.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 192 pix.
= 232.401 Å		1.21 Å/pix.
x 192 pix.
= 232.401 Å		1.21 Å/pix.
x 192 pix.
= 232.401 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21042 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.22632374 - 0.39642027
Average (Standard dev.)0.0007820428 (±0.00994007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 232.40063 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62886_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62886_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62886_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 : SID-1 in complex with dsRNA

EntireName: SID-1 in complex with dsRNA
Components
  • Complex: SID-1 in complex with dsRNA
    • Protein or peptide: Systemic RNA interference defective protein 1
    • RNA: RNA (24-mer)
    • RNA: RNA (24-mer)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

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Supramolecule #1: SID-1 in complex with dsRNA

SupramoleculeName: SID-1 in complex with dsRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 86 KDa

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 86.199133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPQNNSTTPS PIITSSNSSV LVFEISSKMK MIEKKLEANT VHVLRLELDQ SFILDLTKVA AEIVDSSKYS KEDGVILEVT VSNGRDSFL LKLPTVYPNL KLYTDGKLLN PLVEQDFGAH RKRHRIGDPH FHQNLIVTVQ SRLNADIDYR LHVTHLDRAQ Y DFLKFKTG ...String:
GPQNNSTTPS PIITSSNSSV LVFEISSKMK MIEKKLEANT VHVLRLELDQ SFILDLTKVA AEIVDSSKYS KEDGVILEVT VSNGRDSFL LKLPTVYPNL KLYTDGKLLN PLVEQDFGAH RKRHRIGDPH FHQNLIVTVQ SRLNADIDYR LHVTHLDRAQ Y DFLKFKTG QTTKTLSNQK LTFVKPIGFF LNCSEQNISQ FHVTLYSEDD ICANLITVPA NESIYDRSVI SDKTHNRRVL SF TKRADIF FTETEISMFK SFRIFVFIAP DDSGCSTNTS RKSFNEKKKI SFEFKKLENQ SYAVPTALMM IFLTTPCLLF LPI VINIIK NSRKLAPSQS NLISFSPVPS EQRDMDLSHD EQQNTSSELE NNGEIPAAEN QIVEEITAEN QETSVEEGNR EIQV KIPLK QDSLSLHGQM LQYPVAIILP VLMHTAIEFH KWTTSTMANR DEMCFHNHAC ARPLGELRAW NNIITNIGYT LYGAI FIVL SICRRGRHEY SHVFGTYECT LLDVTIGVFM VLQSIASATY HICPSDVAFQ FDTPCIQVIC GLLMVRQWFV RHESPS PAY TNILLVGVVS LNFLISAFSK TSYVRFIIAV IHVIVVGSIC LAKERSLGSE KLKTRFFIMA FSMGNFAAIV MYLTLSA FH LNQIATYCFI INCIMYLMYY GCMKVLHSER ITSKAKLCGA LSLLAWAVAG FFFFQDDTDW TRSAAASRAL NKPCLLLG F FGSHDLWHIF GALAGLFTFI FVSFVDDDLI NTRKTSINIF

UniProtKB: Systemic RNA interference defective protein 1

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Macromolecule #2: RNA (24-mer)

MacromoleculeName: RNA (24-mer) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.576306 KDa
SequenceString:
AAAAAAAAAA A

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Macromolecule #3: RNA (24-mer)

MacromoleculeName: RNA (24-mer) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.322866 KDa
SequenceString:
UUUUUUUUUU U

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #8: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 8 / Number of copies: 2 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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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: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 2793 / Average exposure time: 5.0 sec. / Average electron dose: 62.844 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 227508
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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