8TCA

Structure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification, no ligand

• PDB DOI: https://doi.org/10.2210/pdb8TCA/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-06-30 Released: 2024-02-07 
• Deposition Author(s): Angelo, M.C., Aoki, S.T.
• 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: 2.02 Å
• R-Value Free: 0.224 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification

Angelo, M.C., Aoki, S.T.

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)

Macromolecule Content

• Total Structure Weight: 47.62 kDa 
• Atom Count: 3,562 
• Modelled Residue Count: 425 
• Deposited Residue Count: 436 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
m6A binding IgG Fab, heavy chain	A [auth H]	221	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
m6A binding IgG Fab, light chain	B [auth L]	215	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth H], D [auth H], E [auth H], F [auth H], G [auth H], H [auth L], I [auth L], J [auth L], K [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.224 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.906	α = 90
b = 79.906	β = 90
c = 145.127	γ = 90

Software Package:

Software Name	Purpose
PDB-REDO	refinement
PHENIX	refinement
autoPROC	data processing
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Angelo, M.C., Aoki, S.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R35GM142691

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release