1A4J | pdb_00001a4j

DIELS ALDER CATALYTIC ANTIBODY GERMLINE PRECURSOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.292 (Depositor) 
  • R-Value Work: 
    0.229 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Immunological origins of binding and catalysis in a Diels-Alderase antibody.

Romesberg, F.E.Spiller, B.Schultz, P.G.Stevens, R.C.

(1998) Science 279: 1929-1933

  • DOI: https://doi.org/10.1126/science.279.5358.1929
  • Primary Citation Related Structures: 
    1A4J, 1A4K

  • PubMed Abstract: 

    The three-dimensional structure of an antibody (39-A11) that catalyzes a Diels-Alder reaction has been determined. The structure suggests that the antibody catalyzes this pericyclic reaction through a combination of packing and hydrogen-bonding interactions that control the relative geometries of the bound substrates and electronic distribution in the dienophile. A single somatic mutation, serine-91 of the light chain to valine, is largely responsible for the increase in affinity and catalytic activity of the affinity-matured antibody. Structural and functional studies of the germ-line precursor suggest that 39-A11 and related antibodies derive from a family of germ-line genes that have been selected throughout evolution for the ability of the encoded proteins to form a polyspecific combining site. Germ line-encoded antibodies of this type, which can rapidly evolve into high-affinity receptors for a broad range of structures, may help to expand the binding potential associated with the structural diversity of the primary antibody repertoire.


  • Organizational Affiliation
    • Howard Hughes Medical Institute and the Department of Chemistry, University of California, Berkeley, CA 94720, USA. 94720, USA.

Macromolecule Content 

  • Total Structure Weight: 94.6 kDa 
  • Atom Count: 6,890 
  • Modeled Residue Count: 868 
  • Deposited Residue Count: 872 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)A [auth L],
C [auth A]
217Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
PHAROS:  P01834
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01834
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)B [auth H],
D [auth B]
219Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.292 (Depositor) 
  • R-Value Work:  0.229 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.9α = 90
b = 49.33β = 108.74
c = 145γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary