8ID2: Splicing factor 3A subunit 1

Crystal structure of the ubiquitin-like domain in the SF3A1 subunit of human U2 snRNP complexed with the stem-loop 4 of U1 snRNA. Determined by X-ray diffraction at 1.8 Å resolution. Released 17 May 2023.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,540
Mol. weight: 41.38 kDa
Released: 17 May 2023

Explore 8ID2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ID2 contains 7 α-helices and 18 β-strands across 2 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.

Chain A: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	704	1
β-strand	705-710	6	1
β-strand	713	1	2
β-strand	723	1	2
β-strand	726-731	6	1
β-strand	736	1	3
α-helix	737-748	12
α-helix	752-754	3
β-strand	755-759	5	1
β-strand	762	1	1
β-strand	769	1	3
α-helix	771-773	3
β-strand	779-785	7	1

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	705-710	6	4
β-strand	713	1	5
β-strand	723	1	5
β-strand	726-731	6	4
β-strand	736	1	6
α-helix	738-748	11
α-helix	752-754	3
β-strand	755-759	5	4
β-strand	762-763	2	4
β-strand	769	1	6
α-helix	771-773	3
β-strand	779-785	7	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Splicing factor 3A subunit 1	A, B	protein	117	Homo sapiens	Q15459 (AlphaFold model)
RNA (5'-r(gpgpgpgpapcpupgpcpgpupupcpgpcpgpcpupupupcpcpcpc)-3')	C, D	RNA	24	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>8ID2_1 Splicing factor 3A subunit 1 (chains A, B)
MGSSHHHHHHSSGLVPRGSHENLYFQGPVSIKVQVPNMQDKTEWKLNGQVLVFTLPLTDQ
VSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERGGRKK

Sequence of entity 2 (C, D), FASTA

>8ID2_2 RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*CP*GP*UP*UP*CP*GP*CP*GP*CP*UP*UP*UP*CP*CP*CP*C)-3') (chains C, D)
GGGGACUGCGUUCGCGCUUUCCCC

Primary citation

Structural insights into recognition of SL4, the UUCG stem-loop, of human U1 snRNA by the ubiquitin-like domain, including the C-terminal tail in the SF3A1 subunit of U2 snRNP. Nameki, N., Terawaki, S.I., Takizawa, M. et al. J Biochem (2023) 174:203-216. DOI 10.1093/jb/mvad033 · PubMed

Other PDB entries of the same protein (UniProt Q15459 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P0V 1.56 Å, Crystal structure of human SF3A1 ubiquitin-like domain in complex with U1 snRNA…
7EVO 2.5 Å, The cryo-EM structure of the human 17S U2 snRNP
8H6L 2.6 Å, Cryo-EM structure of human exon-defined spliceosome in the early B state.
8H6K 2.7 Å, Cryo-EM structure of human exon-defined spliceosome in the mature B state.
8HK1 2.7 Å, The cryo-EM structure of human pre-17S U2 snRNP
7VPX 3.0 Å, The cryo-EM structure of the human pre-A complex
8I0R 3.0 Å, The cryo-EM structure of human Bact-I complex
8I0T 3.0 Å, The cryo-EM structure of human Bact-III complex
8Q7N 3.1 Å, cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region)
8QOZ 3.1 Å, Cryo-EM Structure of Pre-B+5'ss+ATPgammaS Complex (core part)
8QPE 3.1 Å, Cryo-EM Structure of Pre-B-like Complex (core part)
8H6E 3.2 Å, Cryo-EM structure of human exon-defined spliceosome in the late pre-B state.

Browse structure collections

About this viewer

MolViewer shows 8ID2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.