9CM4 | pdb_00009cm4

HCV2 Fab bound to selected RNA loop

• PDB DOI: https://doi.org/10.2210/pdb9CM4/pdb
• NAKB: 9CM4

• Classification: RNA binding protein/RNA
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-12 Released: 2026-01-14 
• Deposition Author(s): Disare, M.T., Lewicka, A., Piccirilli, J.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.198 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.160 (Depositor) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

A suite of portable RNA epitopes as structural biology tools

Disare, M.T., Lewicka, A., Krochmal, D., Koirala, D., Piccirilli, J.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 110.16 kDa 
• Atom Count: 8,852 
• Modeled Residue Count: 914 
• Deposited Residue Count: 936 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV2 Fab heavy chain	A [auth H], C [auth A]	233	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV2 fab light chain	B [auth L], D [auth B]	215	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
HCV2 RNA loop	E [auth G], F [auth J]	20	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth L], I [auth L], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	G [auth L], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.198 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.160 (Depositor) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 215.232	α = 90
b = 52.21	β = 124.92
c = 133.338	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-14 
Deposition Author(s): Disare, M.T., Lewicka, A., Piccirilli, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM149336

Revision History  

• Version 1.0: 2026-01-14
  Type: Initial release