3SIV: NHP2-like protein 1

Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, dimeric form. Determined by X-ray diffraction at 3.3 Å resolution. Released 10 Aug 2011.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 12
Atoms: 14,114
Mol. weight: 211.79 kDa
Released: 10 Aug 2011

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

Secondary structure: helices and β-sheets

3SIV contains 83 α-helices and 20 β-strands across 8 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: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	1
α-helix	16-31	16
β-strand	36-37	2	1
α-helix	39-47	9
β-strand	51-57	7	1
α-helix	63-66	4
α-helix	68-75	8
β-strand	80-83	4	1
α-helix	86-92	7
β-strand	101-105	5	1
α-helix	113-127	15

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	154-157	4
α-helix	162-172	11
α-helix	181-215	35
α-helix	217-223	7
α-helix	225-235	11
α-helix	238-243	6
α-helix	246-250	5
α-helix	278-281	4
α-helix	285-287	3
α-helix	288-307	20
α-helix	315-330	16

Chain D: 8 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	36-37	2	2
α-helix	39-47	9
β-strand	51-56	6	2
α-helix	63-66	4
α-helix	69-75	7
β-strand	80-82	3	2
α-helix	86-93	8
β-strand	101-105	5	2
α-helix	113-124	12

Chain E: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	89-118	30
α-helix	123-127	5
α-helix	132-141	10
α-helix	146-149	4
α-helix	153-156	4
α-helix	161-170	10
α-helix	181-215	35
α-helix	217-222	6
α-helix	225-235	11
α-helix	238-242	5
α-helix	246-251	6
α-helix	273-276	4
α-helix	278-281	4
α-helix	287-306	20
α-helix	315-331	17

Chain G: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	3
α-helix	16-31	16
β-strand	35-37	3	3
α-helix	39-47	9
β-strand	51-57	7	3
α-helix	63-66	4
α-helix	68-72	5
β-strand	80-83	4	3
α-helix	86-92	7
β-strand	101-105	5	3
α-helix	113-127	15

Chain H: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	89-116	28
α-helix	134-138	5
α-helix	181-189	9
α-helix	192-215	24
α-helix	217-222	6
α-helix	225-235	11
α-helix	238-241	4
α-helix	246-249	4
α-helix	273-276	4
α-helix	285-287	3
α-helix	288-306	19
α-helix	315-331	17

Chain J: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	4
α-helix	14-15	2
α-helix	16-31	16
β-strand	35-37	3	4
α-helix	39-47	9
β-strand	51-57	7	4
α-helix	63-65	3
α-helix	69-76	8
β-strand	80-83	4	4
α-helix	86-93	8
β-strand	101-105	5	4
α-helix	113-127	15

Chain K: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	89-116	28
α-helix	125-128	4
α-helix	132-142	11
α-helix	153-156	4
α-helix	161-168	8
α-helix	181-208	28
α-helix	212-215	4
α-helix	217-220	4
α-helix	225-235	11
α-helix	239-242	4
α-helix	246-249	4
α-helix	273-276	4
α-helix	278-281	4
α-helix	287-306	20
α-helix	315-329	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NHP2-like protein 1	A, D, G, J	protein	130	Homo sapiens	P55769 (AlphaFold model)
U4/U6 small nuclear ribonucleoprotein Prp31	B, E, H, K	protein	254	Homo sapiens	Q8WWY3 (AlphaFold model)
U4atac snRNA	C, F, I, L	RNA	32	Homo sapiens

Sequence of entity 1 (A, D, G, J), FASTA

>3SIV_1 NHP2-like protein 1 (chains A, D, G, J)
GSMTEADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAA
DAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQS
IQQSIERLLV

Sequence of entity 2 (B, E, H, K), FASTA

>3SIV_2 U4/U6 small nuclear ribonucleoprotein Prp31 (chains B, E, H, K)
GPLGSEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTV
KELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNA
SKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQRKTL
SGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYE
LKDEIERKFDKWQE

Sequence of entity 3 (C, F, I, L), FASTA

>3SIV_3 U4atac snRNA (chains C, F, I, L)
UACUGUCCAAUGAGCGCAUAGUGAGGGCAGUA

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.
3SIU 2.63 Å, Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, monomeric form
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.

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