7W2P: Tudor domain of SMN

Tudor domain of SMN in complex with a small molecule. Determined by X-ray diffraction at 1.15 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 1.15 Å
Organism: Homo sapiens
Chains: 1
Atoms: 623
Mol. weight: 7.68 kDa
Ligands: 8AI, MG
Released: 5 Oct 2022

Explore 7W2P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7W2P contains 4 α-helices and 5 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: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	87-89	3
β-strand	97-102	6	1
α-helix	103-105	3
β-strand	107-117	11	1
β-strand	122-127	6	1
β-strand	133-137	5	1
α-helix	138-140	3
β-strand	142	1	1
α-helix	143-146	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Survival motor neuron protein	A	protein	66	Homo sapiens	Q16637 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7W2P_1 Survival motor neuron protein (chains A)
KKNTAASLQQWKVGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDL
LSPICE

Ligands and cofactors

ID	Name	Formula	Copies
8AI	2-[(4-fluorophenyl)methyl]-2-azatricyclo[7.3.0.0^{3,7}]dodeca-1(9),3(7)-dien-8-…	C18 H19 F N2	1
MG	Magnesium ion	Mg	2

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

Primary citation

A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II. Liu, Y., Iqbal, A., Li, W. et al. Nat Commun (2022) 13:5453-5453. DOI 10.1038/s41467-022-33229-5 · PubMed

Other PDB entries of the same protein (UniProt Q16637 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QQ6 1.75 Å, Crystal Structure of tudor domain of SMN1 in complex with a small organic molecule
1MHN 1.8 Å, High resolution crystal structure of the SMN Tudor domain
7W30 1.8 Å, Tudor domain of SMN in complex with a small molecule
4GLI 1.9 Å, Crystal Structure of Human SMN YG-Dimer
5XJL 2.5 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with…
5XJU 2.58 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with…
5XJT 2.92 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with…
5XJR 3.12 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with…
5XJQ 3.28 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with…
5XJS 3.38 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with…
1G5V Solution structure of the tudor domain of the human smn protein
2LEH Solution structure of the core SMN-Gemin2 complex

Browse structure collections

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