7T0K

Crystal structure of S25-2 Fab Unliganded 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Antigen binding by conformational selection in near-germline antibodies.

Blackler, R.J.Muller-Loennies, S.Pokorny-Lehrer, B.Legg, M.S.G.Brade, L.Brade, H.Kosma, P.Evans, S.V.

(2022) J Biol Chem 298: 101901-101901

  • DOI: https://doi.org/10.1016/j.jbc.2022.101901
  • Primary Citation of Related Structures:  
    7T0F, 7T0G, 7T0H, 7T0I, 7T0J, 7T0K

  • PubMed Abstract: 

    Conformational flexibility in antibody-combining sites has been hypothesized to facilitate polyspecificity toward multiple unique epitopes and enable the limited germline repertoire to match an overwhelming diversity of potential antigens; however, elucidating the mechanisms of antigen recognition by flexible antibodies has been understandably challenging. Here, multiple liganded and unliganded crystal structures of the near-germline anticarbohydrate antibodies S25-2 and S25-39 are reported, which reveal an unprecedented diversity of complementarity-determining region H3 conformations in apparent equilibrium. These structures demonstrate that at least some germline or near-germline antibodies are flexible entities sensitive to their chemical environments, with conformational selection available as an evolved mechanism that preserves the inherited ability to recognize common pathogens while remaining adaptable to new threats.


  • Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria British Columbia, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S25-2 Fab light chainA [auth L],
C [auth A],
E [auth C],
G [auth E]
219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S25-2 Fab heavy chainB [auth H],
D [auth B],
F [auth D],
H [auth F]
223Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth E],
I [auth L],
IA [auth E],
J [auth L],
JA [auth E],
K [auth L],
KA [auth E],
L,
LA [auth F],
M [auth L],
MA [auth F],
N [auth H],
NA [auth F],
O [auth H],
OA [auth F],
P [auth H],
PA [auth F],
Q [auth H],
R [auth H],
S [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth C],
Z [auth C]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.558α = 90
b = 135.497β = 94.26
c = 73.977γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Austria--
Austrian Science FundAustriaP 24021
Austrian Science FundAustriaP 26919

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description