8T9B

Structure of the CK variant of Fab F1 (FabC-F1) in complex with the C-terminal FN3 domain of EphA2

• PDB DOI: https://doi.org/10.2210/pdb8T9B/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-06-23 Released: 2024-05-01 
• Deposition Author(s): Singer, A.U., Bruce, H.A., Enderle, L., Blazer, L., Adams, J.J., Sicheri, F., Sidhu, S.S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.315 
• R-Value Work: 0.296 
• R-Value Observed: 0.297 

Starting Models: experimental, in silico

Literature

Engineered Antigen-binding Fragments for Enhanced Crystallization of Antibody:Antigen Complexes

Bruce, H.A., Singer, A.U., Filippova, E., Blazer, L., Adams, J.J., Enderle, L., Ben-David, M., Radley, E., Mao, D., Pau, V., Orlicky, S., Sicheri, S., Kourinov, I., Atwell, S., Kossiakoff, A.A., Sidhu, S.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 238.49 kDa 
• Atom Count: 15,657 
• Modelled Residue Count: 2,116 
• Deposited Residue Count: 2,196 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CK variant of Fab F1 heavy chain	A [auth C], C [auth A], E [auth D], G [auth F]	237	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CK variant of Fab F1 light chain	B [auth G], D [auth B], F [auth E], H	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	I, J, K, L	98	Homo sapiens	Mutation(s): 0  Gene Names: EPHA2, ECK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens) Explore P29317  Go to UniProtKB:  P29317
PHAROS:  P29317 GTEx:  ENSG00000142627

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.315 
• R-Value Work: 0.296 
• R-Value Observed: 0.297 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.661	α = 90
b = 130.65	β = 89.76
c = 222.996	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Singer, A.U., Bruce, H.A., Enderle, L., Blazer, L., Adams, J.J., Sicheri, F., Sidhu, S.S.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Structure summary