3SIU: NHP2-like protein 1

Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, monomeric form. Determined by X-ray diffraction at 2.63 Å resolution. Released 10 Aug 2011.

Method: X-ray diffraction
Resolution: 2.63 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,896
Mol. weight: 103.55 kDa
Released: 10 Aug 2011

Explore 3SIU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SIU contains 47 α-helices and 10 β-strands across 4 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: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	1
α-helix	14	1
α-helix	16-31	16
β-strand	35-37	3	1
α-helix	39-48	10
β-strand	51-57	7	1
α-helix	63-66	4
α-helix	68-76	9
β-strand	80-83	4	1
α-helix	86-92	7
β-strand	101-105	5	1
α-helix	106	1
α-helix	113-126	14

Chain B: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	89-118	30
α-helix	125-128	4
α-helix	132-142	11
α-helix	149-151	3
α-helix	161-171	11
α-helix	177-180	4
α-helix	181-215	35
α-helix	217-235	19
α-helix	238-242	5
α-helix	246-249	4
α-helix	278-281	4
α-helix	285-287	3
α-helix	288-307	20
α-helix	315-331	17

Chain D: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	13	1	2
α-helix	14-15	2
α-helix	16-31	16
β-strand	35-37	3	2
α-helix	39-47	9
β-strand	51-57	7	2
α-helix	63-65	3
α-helix	68-76	9
β-strand	80-83	4	2
α-helix	86-92	7
β-strand	101-105	5	2
α-helix	106	1
α-helix	113-126	14

Chain E: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	89-117	29
α-helix	125-128	4
α-helix	132-142	11
α-helix	146-148	3
α-helix	153-158	6
α-helix	161-170	10
α-helix	178-180	3
α-helix	181-215	35
α-helix	217-223	7
α-helix	225-235	11
α-helix	238-242	5
α-helix	246-249	4
α-helix	273-276	4
α-helix	278-281	4
α-helix	285-306	22
α-helix	315-331	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NHP2-like protein 1	A, D	protein	130	Homo sapiens	P55769 (AlphaFold model)
U4/U6 small nuclear ribonucleoprotein Prp31	B, E	protein	254	Homo sapiens	Q8WWY3 (AlphaFold model)
U4atac snRNA	C, F	RNA	28	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>3SIU_1 NHP2-like protein 1 (chains A, D)
GSMTEADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAA
DAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQS
IQQSIERLLV

Sequence of entity 2 (B, E), FASTA

>3SIU_2 U4/U6 small nuclear ribonucleoprotein Prp31 (chains B, E)
GPLGSEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTV
KELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNA
SKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQRKTL
SGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYE
LKDEIERKFDKWQE

Sequence of entity 3 (C, F), FASTA

>3SIU_3 U4atac snRNA (chains C, F)
CUGUCCAAUGAGCGCAUAGUGAGGGCAG

Primary citation

Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31. Liu, S., Ghalei, H., Luhrmann, R. et al. RNA (2011) 17:1655-1663. DOI 10.1261/rna.2690611 · PubMed

Other PDB entries of the same protein (UniProt P55769 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OZB 2.6 Å, Structure of a human Prp31-15.5K-U4 snRNA complex
8H6L 2.6 Å, Cryo-EM structure of human exon-defined spliceosome in the early B state.
7MQA 2.7 Å, Cryo-EM structure of the human SSU processome, state post-A1
8H6K 2.7 Å, Cryo-EM structure of human exon-defined spliceosome in the mature B state.
1E7K 2.9 Å, Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment
6QW6 2.92 Å, Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.
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.
8H6J 3.25 Å, Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state.
6QX9 3.28 Å, Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).

Browse structure collections

About this viewer

MolViewer shows 3SIU 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.