Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A4B4C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A4B4C1D1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 195.17 kDa 
• Atom Count: 13,773 
• Modelled Residue Count: 1,746 
• Deposited Residue Count: 1,808 
• Unique protein chains: 3

 4YHP

Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide

• PDB DOI:  https://doi.org/10.2210/pdb4YHP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-27 Released: 2016-02-10 
• Deposition Author(s): Hattori, T., Dementieva, I.S., Montano, S.P., Koide, S.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.250 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation.

Hattori, T., Lai, D., Dementieva, I.S., Montano, S.P., Kurosawa, K., Zheng, Y., Akin, L.R., Swist-Rosowska, K.M., Grzybowski, A.T., Koide, A., Krajewski, K., Strahl, B.D., Kelleher, N.L., Ruthenburg, A.J., Koide, S.

(2016) Proc Natl Acad Sci U S A 113: 2092-2097

• PubMed: 26862167 
• DOI: https://doi.org/10.1073/pnas.1522691113
• Primary Citation of Related Structures:  
  4YHP, 4YHY, 4YHZ


• PubMed Abstract: 
  

Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. This "antigen clasping" produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody-antigen recognition and suggests a strategy for developing extremely specific antibodies.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K9me3 peptide	A [auth P], D [auth Q]	16	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Heavy Chain	B [auth A], E [auth C], G [auth E], H	229	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Light Chain	C [auth B], F [auth D], I [auth L], J [auth F]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	A [auth P], D [auth Q]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.250 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.773	α = 90
b = 159.885	β = 90.01
c = 128.759	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Hattori, T., Dementieva, I.S., Montano, S.P., Koide, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	R21 DA025725
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	RC1 DA028779

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-02-17
  Changes: Database references
• Version 1.2: 2016-03-02
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence