7T0K | pdb_00007t0k

Crystal structure of S25-2 Fab Unliganded 4

PDB DOI: https://doi.org/10.2210/pdb7T0K/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Mus musculus
Mutation(s): No

Deposited: 2021-11-29 Released: 2022-04-20
Deposition Author(s): Legg, M.S.G., Blackler, R.J., Evans, S.V.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.255 (Depositor), 0.258 (DCC)
R-Value Work:
0.222 (Depositor), 0.226 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 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 Biological Chem 298: 101901-101901

PubMed: 35395245 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2022.101901
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 198.01 kDa
Atom Count: 13,900
Modeled Residue Count: 1,752
Deposited Residue Count: 1,768
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S25-2 Fab light chain	A [auth L], C [auth A], E [auth C], G [auth E]	219	Mus musculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S25-2 Fab heavy chain	B [auth H], D [auth B], F [auth D], H [auth F]	223	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth E] SDF format, chain I [auth L] SDF format, chain IA [auth E] SDF format, chain J [auth L] SDF format, chain JA [auth E] SDF format, chain K [auth L] SDF format, chain KA [auth E] SDF format, chain L SDF format, chain LA [auth F] SDF format, chain M [auth L] SDF format, chain MA [auth F] SDF format, chain N [auth H] SDF format, chain NA [auth F] SDF format, chain O [auth H] SDF format, chain OA [auth F] SDF format, chain P [auth H] SDF format, chain PA [auth F] SDF format, chain Q [auth H] SDF format, chain R [auth H] SDF format, chain S [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth L] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth L] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth L] MOL2 format, chain KA [auth E] MOL2 format, chain L MOL2 format, chain LA [auth F] MOL2 format, chain M [auth L] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth H] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth H] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth H] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth H] MOL2 format, chain S [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth L] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth L] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth L] mmCIF format, chain KA [auth E] mmCIF format, chain L mmCIF format, chain LA [auth F] mmCIF format, chain M [auth L] mmCIF format, chain MA [auth F] mmCIF format, chain N [auth H] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth H] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth H] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth H] mmCIF format, chain R [auth H] mmCIF format, chain S [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	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		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain I [auth L] Focus chain IA [auth E] Focus chain J [auth L] Focus chain JA [auth E] Focus chain K [auth L] Focus chain KA [auth E] Focus chain L Focus chain LA [auth F] Focus chain M [auth L] Focus chain MA [auth F] Focus chain N [auth H] Focus chain NA [auth F] Focus chain O [auth H] Focus chain OA [auth F] Focus chain P [auth H] Focus chain PA [auth F] Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain I [auth L] Focus chain IA [auth E] Focus chain J [auth L] Focus chain JA [auth E] Focus chain K [auth L] Focus chain KA [auth E] Focus chain L Focus chain LA [auth F] Focus chain M [auth L] Focus chain MA [auth F] Focus chain N [auth H] Focus chain NA [auth F] Focus chain O [auth H] Focus chain OA [auth F] Focus chain P [auth H] Focus chain PA [auth F] Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth C]