9ODB | pdb_00009odb

Clone 2.1 Fab in complex with chicken IgY CH2 domain (local refinement)

• PDB DOI: https://doi.org/10.2210/pdb9ODB/pdb
• EM Map EMD-70353: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Gallus gallus, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-04-26 Released: 2025-06-11 
• Deposition Author(s): Ozorowski, G., Alkutkar, T., Ward, A.B.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Replaying germinal center evolution on a quantified affinity landscape.

DeWitt, W.S., Vora, A.A., Araki, T., Galloway, J.G., Alkutkar, T., Bortolatto, J., Castro, T.B.R., Dumm, W., Jennings-Shaffer, C., Jia, T., Mesin, L., Ozorowski, G., Pae, J., Ralph, D.K., Bloom, J.D., Nourmohammad, A., Song, Y.S., Ward, A.B., Starr, T.N., Matsen, F.A., Victora, G.D.

(2025) bioRxiv 

• PubMed: 40661619 
• DOI: https://doi.org/10.1101/2025.06.02.656870
• Primary Citation of Related Structures:  
  9ODB


• PubMed Abstract: 
  

  Darwinian evolution of immunoglobulin genes within germinal centers (GC) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the mechanics of how competition between GC B cells drives increased affinity are well established, the dynamical evolutionary features of this process remain poorly characterized. We devised an experimental evolution model in which we "replay" over one hundred instances of a clonally homogenous GC reaction and follow the selective process by assigning affinities to all cells using deep mutational scanning. Our data reveal how GCs achieve predictable evolutionary outcomes through the cumulative effects of many rounds of imperfect selection, acting on a landscape shaped heavily by somatic hypermutation (SHM) targeting biases. Using time-calibrated models, we show that apparent features of GC evolution such as permissiveness to low-affinity lineages and early plateauing of affinity are best explained by survivorship biases that distort our view of how affinity progresses over time.

---

Organizational Affiliation: 
• Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.
Present address: BioMedicine Design, Pfizer, Cambridge, MA, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
Howard Hughes Medical Institute, New York, NY, USA.
Howard Hughes Medical Institute, Seattle, WA, USA.
Department of Physics, University of Washington, Seattle, WA, USA.
Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA.
Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
Department of Statistics, University of California, Berkeley, CA, USA.
Computer Science Division, University of California, Berkeley, CA, USA.
Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.
Department of Statistics, University of Washington, Seattle, WA, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 218.46 kDa 
• Atom Count: 4,862 
• Modeled Residue Count: 631 
• Deposited Residue Count: 2,028 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chicken IgY heavy chain,Ig-like domain-containing protein	A, F [auth D]	561	Gallus gallus	Mutation(s): 2
UniProt
Find proteins for A0A8V0XLK0 (Gallus gallus) Explore A0A8V0XLK0  Go to UniProtKB:  A0A8V0XLK0
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Clone 2.1 Fab heavy chain	B [auth H], D [auth B]	239	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Clone 2.1 Fab light chain	C [auth L], E [auth C]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Ozorowski, G., Alkutkar, T., Ward, A.B.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release
  
• Version 1.1: 2025-07-30
  Changes: Data collection, Database references