9L8M | pdb_00009l8m

Structure of SID-1 in complex with dsRNA

• PDB DOI: https://doi.org/10.2210/pdb9L8M/pdb
• NAKB: 9L8M
• EM Map EMD-62886: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/RNA
• Organism(s): Caenorhabditis elegans, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-12-27 Released: 2026-01-21 
• Deposition Author(s): Kumazaki, K., Kusakizako, T., Nishizawa, T., Nureki, O.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into SID1-mediated dsRNA uptake: A self-organizing endocytic mechanism

Takai, A., Kumazaki, K., Awazu, T., Kambara, T., Murakoshi, S., Kato, T., Hiraizumi, M., Kise, Y., Kusakizako, T., Nishizawa, T., Okada, T., Nureki, O.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 96.24 kDa 
• Atom Count: 5,652 
• Modeled Residue Count: 653 
• Deposited Residue Count: 783 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Systemic RNA interference defective protein 1	A	761	Caenorhabditis elegans	Mutation(s): 0  Gene Names: sid-1, rde-7, rsd-8, C04F5.1
UniProt
Find proteins for Q9GZC8 (Caenorhabditis elegans) Explore Q9GZC8  Go to UniProtKB:  Q9GZC8
Glycosylation
Glycosylation Sites: 3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (24-mer)	B [auth C]	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (24-mer)	C [auth D]	11	synthetic construct

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B], E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LBN	I [auth A], J [auth A]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C42 H82 N O8 P WTJKGGKOPKCXLL-VYOBOKEXSA-N
Y01	H [auth A]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat	0.4.88
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Kumazaki, K., Kusakizako, T., Nishizawa, T., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H05037
Japan Science and Technology	Japan	JPMJCR20E2
Japan Agency for Medical Research and Development (AMED)	Japan	JP19am01011115

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release