2OZB: Human Prp31-15.5K-U4 snRNA complex

Structure of a human Prp31-15.5K-U4 snRNA complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 20 Mar 2007.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,375
Mol. weight: 107.81 kDa
Ligands: CA
Released: 20 Mar 2007

Explore 2OZB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OZB contains 43 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: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	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	63-65	3
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	113-124	12

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	146-148	3
α-helix	155-157	3
α-helix	161-172	12
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: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	2
α-helix	14	1
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	113-126	14

Chain E: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	89-118	30
α-helix	125-128	4
α-helix	132-142	11
α-helix	155-158	4
α-helix	161-171	11
α-helix	178-180	3
α-helix	181-215	35
α-helix	217-235	19
α-helix	238-241	4
α-helix	246-249	4
α-helix	267-268	2
α-helix	278-281	4
α-helix	285-287	3
α-helix	288-307	20
α-helix	315-331	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA comprising the 5' Stem-Loop RNA of U4snRNA	C, F	RNA	33
U4/U6.U5 tri-snRNP 15.5 kDa protein	A, D	protein	130	Homo sapiens	P55769 (AlphaFold model)
U4/U6 small nuclear ribonucleoprotein Prp31	B, E	protein	260	Homo sapiens	Q8WWY3 (AlphaFold model)

Sequence of entity 1 (C, F), FASTA

>2OZB_1 RNA comprising the 5' Stem-Loop RNA of  U4snRNA (chains C, F)
AUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAU

Sequence of entity 2 (A, D), FASTA

>2OZB_2 U4/U6.U5 tri-snRNP 15.5 kDa protein (chains A, D)
GSMTEADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAA
DAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQS
IQQSIERLLV

Sequence of entity 3 (B, E), FASTA

>2OZB_3 U4/U6 small nuclear ribonucleoprotein Prp31 (chains B, E)
GPLGSEVMGPVEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNAL
DYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDM
ALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLG
AQRKTLSGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTE
GKVGYELKDEIERKFDKWQE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Primary citation

Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP. Liu, S., Li, P., Dybkov, O. et al. Science (2007) 316:115-120. DOI 10.1126/science.1137924 · PubMed

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

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.
6QX9 3.28 Å, Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).

Browse structure collections

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