8PEQ

Complex of diubiquitin-derived artificial binding protein (Affilin) variant Af2 with its target oncofetal fibronectin (fragment 7B8)

• PDB DOI: https://doi.org/10.2210/pdb8PEQ/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-06-14 Released: 2024-06-26 
• Deposition Author(s): Parthier, C., Katzschmann, A., Fiedler, E., Haupts, U., Reimann, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.251 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

Ubiquitin-derived artificial binding proteins targeting oncofetal fibronectin reveal scaffold plasticity by beta-strand slippage

Katzschmann, A., Fiedler, E., Haupts, U., Reimann, A., Settele, F., Gloser-Braeunig, M., Parthier, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 141.91 kDa 
• Atom Count: 10,486 
• Modelled Residue Count: 1,278 
• Deposited Residue Count: 1,284 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibronectin	A, B, C	275	Homo sapiens	Mutation(s): 1  Gene Names: FN1, FN
UniProt & NIH Common Fund Data Resources
Find proteins for P02751 (Homo sapiens) Explore P02751  Go to UniProtKB:  P02751
PHAROS:  P02751 GTEx:  ENSG00000115414

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Affilin variant Af2	D [auth J], E [auth L], F [auth M]	153	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.251 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.65	α = 90
b = 105.856	β = 93.53
c = 78.993	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Parthier, C., Katzschmann, A., Fiedler, E., Haupts, U., Reimann, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release