9YXV | pdb_00009yxv

Cryo-EM structure of the core region of cIL-U1A-Fab1R-PGA1-sfFab quaternary complex at 2.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb9YXV/pdb
• EM Map EMD-73618: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct, Streptococcus sp. 'group G
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-10-27 Released: 2026-05-27 
• Deposition Author(s): Filippova, E.V., Kossiakoff, A.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

Starting Models: experimental

Literature

A universal Fab targeting a conserved U1A-RNA epitope for RNA structure determination by cryo-EM

Filippova, E.V., Krochmal, D., Mukherjee, S., Piccirilli, J.A., Kossiakoff, A.A.

(2026) Nucleic Acids Res 54

• DOI: https://doi.org/10.1093/nar/gkag502

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 127.87 kDa 
• Atom Count: 6,554 
• Modeled Residue Count: 825 
• Deposited Residue Count: 1,138 
• Unique protein chains: 6
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	A	97	Homo sapiens	Mutation(s): 2  Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012  Go to UniProtKB:  P09012
PHAROS:  P09012 GTEx:  ENSG00000077312

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein G	C	67	Streptococcus sp. 'group G	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
sfFab18 light chain	D	239	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
sfFab18 heavy chain	E	234	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab1R heavy chain	F [auth H]	264	Homo sapiens	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab1R light chain	G [auth L]	219	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Hairpin II of the U1 snRNA (U1hpII)	B	18	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMU (Subject of Investigation/LOI)	H [auth A]	DECYL-BETA-D-MALTOPYRANOSIDE C22 H42 O11 WOQQAWHSKSSAGF-WXFJLFHKSA-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	PHENIX
MODEL REFINEMENT	Coot
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Filippova, E.V., Kossiakoff, A.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release