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- EMDB-62887: Structure of SID-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-62887
TitleStructure of SID-1
Map dataFSC-weighted, sharpened and masked map by PostProcess
Sample
  • Complex: SID-1
    • Protein or peptide: Systemic RNA interference defective protein 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
KeywordsMembrane protein
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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_62887.png

Downloads & links

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Map

FileDownload / File: emd_62887.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFSC-weighted, sharpened and masked map by PostProcess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.092885375 - 0.13605677
Average (Standard dev.)0.0003203197 (±0.003598059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62887_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62887_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_62887_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

EntireName: SID-1
Components
  • Complex: SID-1
    • Protein or peptide: Systemic RNA interference defective protein 1
  • 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

SupramoleculeName: SID-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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 #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / 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 #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #6: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 6 / 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
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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2476 / Average exposure time: 2.6 sec. / Average electron dose: 49.6 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

Particle selectionNumber selected: 1495868
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 30549
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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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Details: SID-1 protein in our accompanying PDB entry "SID-1 in complex with dsRNA"
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9l8n:
Structure of SID-1

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