4YHZ

Crystal structure of 304M3-B Fab in complex with H3K4me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.304 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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.USA 113: 2092-2097

  • DOI: 10.1073/pnas.1522691113
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab Heavy Chain
H
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab Light Chain
L
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
H3K4me3 peptide
P
12Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
H, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
P
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.304 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.375α = 90.00
b = 130.375β = 90.00
c = 96.365γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug AbuseUnited StatesR21 DA025725
National Institutes of Health/National Institute on Drug AbuseUnited StatesRC1 DA028779

Revision History 

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