9DOC: PDB entry 9DOC

The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Thr-Val linker variant, at 1.2 Angstrom resolution. Determined by X-ray diffraction at 1.19 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 1.19 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,341
Mol. weight: 30.8 kDa
Ligands: MG, PO4
Released: 6 Nov 2024

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

Secondary structure: helices and β-sheets

9DOC contains 17 α-helices and 6 β-strands across 1 chain. 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.

Chain A: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	24-26	3
α-helix	29-43	15
α-helix	45-49	5
α-helix	57-60	4
α-helix	65-71	7
α-helix	76-88	13
β-strand	94-101	8	1
α-helix	104-109	6
α-helix	110-123	14
β-strand	129-136	8	1
β-strand	140-147	8	1
α-helix	150-161	12
α-helix	171-185	15
α-helix	187-189	3
β-strand	192-198	7	1
α-helix	206-219	14
β-strand	223-228	6	1
α-helix	234-240	7
α-helix	244-246	3
β-strand	247-249	3	1
α-helix	250-252	3
α-helix	253-265	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor ETV6,Capillary morphogenesis gene 2 protein	A	protein	268	Homo sapiens	P41212 (AlphaFold model), P58335 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9DOC_1 Transcription factor ETV6,Capillary morphogenesis gene 2 protein (chains A)
MGHHHHHHHHHHSIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLSPIDSNTFEMNGKAL
LLLTKEDFRYRSPHSGDELYELLQHILAQARTVFDLYFVLDKSGSVANNWIEIYNFVQQL
AERFVSPEMRLSFIVFSSQATIILPLTGDRGKISKGLEDLKRVSPVGETYIHEGLKLANE
QIQKAGGLKTSSIIIALTDGKLDGLVPSYAEKEAKISRSLGASVYAVGVLDFEQAQLERI
ADSKEQVFPVKGGFQALKGIINSILAQS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	7
PO4	Phosphate ion	O4 P	2

Water and common crystallization additives (NA, GOL) are not listed.

Primary citation

1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons. Samarawickrama, P., Ludlow, K., Probst, R. 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:

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
8THA 1.68 Å, 1TEL, non-compressed, double-helical crystal form

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