9YKB | pdb_00009ykb

The von Willebrand factor A domain of human capillary morphogenesis gene II, fused to the 1TEL crystallization chaperone, Ala-Val linker variant, expressed with SUMO tag.

• PDB DOI: https://doi.org/10.2210/pdb9YKB/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-10-06 Released: 2025-10-22 
• Deposition Author(s): Gajjar, P., Samarawickrama, P., Pedroza Romo, M.J., Keliiliki, A., Litchfield, C., Callahan, M., Redd, N., Doukov, T., Lebedev, A., Moody, J.D.
• Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons

Samarawickrama, P., Mead, D., Ludlow, K., Probst, R., Doukov, T., Moody, J.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: electron microscopy

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 86.16 kDa 
• Atom Count: 6,220 
• Modeled Residue Count: 763 
• Deposited Residue Count: 771 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor ETV6,Anthrax toxin receptor 2	A, B [auth C], C [auth B]	257	Homo sapiens	Mutation(s): 6  Gene Names: ETV6, TEL, TEL1, ANTXR2, CMG2
UniProt & NIH Common Fund Data Resources
Find proteins for P41212 (Homo sapiens) Explore P41212  Go to UniProtKB:  P41212
PHAROS:  P41212 GTEx:  ENSG00000139083
Find proteins for P58335 (Homo sapiens) Explore P58335  Go to UniProtKB:  P58335
PHAROS:  P58335 GTEx:  ENSG00000163297
UniProt Groups	P41212P58335

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], E [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.745	α = 90
b = 163.745	β = 90
c = 54.246	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Gajjar, P., Samarawickrama, P., Pedroza Romo, M.J., Keliiliki, A., Litchfield, C., Callahan, M., Redd, N., Doukov, T., Lebedev, A., Moody, J.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	1R15GM146209, 1R35GM155011

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release