9YKB: PDB entry 9YKB

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. Determined by X-ray diffraction at 2.5 Å resolution. Released 22 Oct 2025.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,220
Mol. weight: 86.16 kDa
Ligands: MG
Released: 22 Oct 2025

Explore 9YKB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YKB contains 48 α-helices and 18 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and C: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	7-10	4
α-helix	13-15	3
α-helix	18-31	14
α-helix	34-36	3
α-helix	46-49	4
α-helix	54-60	7
α-helix	65-78	14
β-strand	83-90	8	1
α-helix	93-95	3
α-helix	99-113	15
β-strand	118-125	8	1
β-strand	129-136	8	1
α-helix	139-150	12
α-helix	160-174	15
β-strand	180-187	8	1
α-helix	195-208	14
β-strand	212-217	6	1
α-helix	223-229	7
α-helix	233-235	3
β-strand	236-238	3	1
α-helix	242-254	13

Chain B: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	13-15	3
α-helix	18-31	14
α-helix	34-36	3
α-helix	46-49	4
α-helix	54-60	7
α-helix	65-77	13
β-strand	83-90	8	3
α-helix	93-95	3
α-helix	99-112	14
β-strand	118-125	8	3
β-strand	129-136	8	3
α-helix	139-150	12
α-helix	160-173	14
β-strand	180-187	8	3
α-helix	195-208	14
α-helix	211	1
β-strand	212-217	6	3
α-helix	223-229	7
α-helix	233-235	3
β-strand	236-238	3	3
α-helix	239-254	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor ETV6,Anthrax toxin receptor 2	A, B, C	protein	257	Homo sapiens	P41212 (AlphaFold model), P58335 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>9YKB_1 Transcription factor ETV6,Anthrax toxin receptor 2 (chains A, B, C)
GSIALPAHLRLQPIYWSRDDVAQWLKWAENEFSLRPIDSNTFEMNGKALLLLTKEDFRYR
SPHSGDELYELLQHILAQARAVFDLYFVLDKSGSVANNWIEIYNFVQQLAERFVSPEMRL
SFIVFSSQATIILPLTGDRGKISKGLEDLKRVSPVGETYIHEGLKLANEQIQKAGGLKTS
SIIIALTDGKLDGLVPSYAEKEAKISRSLGASVYAVGVLDFEQAQLERIADSKEQVFPVK
GGFQALKGIINSILAQS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4

Water and common crystallization additives (CL) are not listed.

Primary citation

1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons. Samarawickrama, P., Mead, D., Ludlow, K. et al. To be published.

Other PDB entries of the same protein (UniProt P41212 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9DOC 1.19 Å, The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly…
9ZB7 1.24 Å, A DARPin fused to the 1TEL crystallization chaperone via a direct helical fusion
9Q4D 1.3 Å, A DARPin fused to the double trigger 1TEL variant crystallization chaperone via a direct…
7TW9 1.41 Å, Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to Sinefungin
1JI7 1.45 Å, Crystal Structure of TEL SAM Polymer
7TDY 1.53 Å, The ubiquitin-associated domain of human thirty-eight negative kinase 1, flexibly fused…
7TW8 1.55 Å, Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SAH
8FRJ 1.57 Å, Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SGC0946
9DB5 1.57 Å, A DARPin fused to the 1TEL crystallization chaperone via a proline-alanine linker
8FT8 1.6 Å, The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly…
8FRK 1.61 Å, Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SGC8158
7TW7 1.62 Å, Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SAM

Browse structure collections

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