4NWT

Crystal structure of the anti-human NGF Fab APE1531


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies.

Bowers, P.M.Verdino, P.Wang, Z.da Silva Correia, J.Chhoa, M.Macondray, G.Do, M.Neben, T.Y.Horlick, R.A.Stanfield, R.L.Wilson, I.A.King, D.J.

(2014) J.Biol.Chem. 289: 33557-33567

  • DOI: 10.1074/jbc.M114.607176
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • During somatic hypermutation (SHM), deamination of cytidine by activation-induced cytidine deaminase and subsequent DNA repair generates mutations within immunoglobulin V-regions. Nucleotide insertions and deletions (indels) have recently been shown ...

    During somatic hypermutation (SHM), deamination of cytidine by activation-induced cytidine deaminase and subsequent DNA repair generates mutations within immunoglobulin V-regions. Nucleotide insertions and deletions (indels) have recently been shown to be critical for the evolution of antibody binding. Affinity maturation of 53 antibodies using in vitro SHM in a non-B cell context was compared with mutation patterns observed for SHM in vivo. The origin and frequency of indels seen during in vitro maturation were similar to that in vivo. Indels are localized to CDRs, and secondary mutations within insertions further optimize antigen binding. Structural determination of an antibody matured in vitro and comparison with human-derived antibodies containing insertions reveal conserved patterns of antibody maturation. These findings indicate that activation-induced cytidine deaminase acting on V-region sequences is sufficient to initiate authentic formation of indels in vitro and in vivo and that point mutations, indel formation, and clonal selection form a robust tripartite system for antibody evolution.


    Organizational Affiliation

    From Anaptysbio Inc., San Diego, California 92121 and pbowers@anaptysbio.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APE1531 Ab Fab light chain
L
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
APE1531 Ab Fab heavy chain
H
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
H, L
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
H
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
L
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 127.720α = 90.00
b = 64.360β = 108.67
c = 63.810γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
WEB-ICEdata collection
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Database references
  • Version 1.2: 2014-12-10
    Type: Database references
  • Version 1.3: 2017-08-02
    Type: Refinement description, Source and taxonomy