1SYX: Binary U5 snRNP complex

The crystal structure of a binary U5 snRNP complex. Determined by X-ray diffraction at 2.35 Å resolution. Released 18 Oct 2005.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,082
Mol. weight: 80.05 kDa
Released: 18 Oct 2005

Explore 1SYX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1SYX contains 27 α-helices and 36 β-strands across 6 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	7-8	2	1
α-helix	11-19	9
β-strand	25-31	7	1
α-helix	36-48	13
β-strand	56-62	7	1
α-helix	67-69	3
α-helix	70-73	4
β-strand	80-85	6	1
β-strand	88-90	3	1
β-strand	91-93	3	2
β-strand	102	1	1
α-helix	109-124	16
β-strand	129-131	3	2

Chains B and F: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	27-31	5	7
α-helix	39-40	2
β-strand	41-45	5	7
α-helix	46-54	9
β-strand	63-66	4	7
β-strand	75-76	2	7
α-helix	77-79	3
α-helix	82-85	4

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	3
α-helix	11-19	9
β-strand	25-31	7	3
α-helix	36-52	17
β-strand	56-62	7	3
α-helix	70-73	4
β-strand	80-85	6	3
β-strand	88-90	3	3
β-strand	91-93	3	4
β-strand	102	1	3
α-helix	109-124	16
β-strand	129-131	3	4

Chain D: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	27-31	5	8
α-helix	39-40	2
β-strand	41-45	5	8
α-helix	46-53	8
β-strand	63-66	4	8
β-strand	75-76	2	8
α-helix	77-79	3
α-helix	82-85	4

Chain E: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	5
α-helix	11-19	9
β-strand	25-31	7	5
α-helix	36-48	13
β-strand	56-62	7	5
α-helix	67-69	3
α-helix	70-73	4
β-strand	80-85	6	5
β-strand	88-90	3	5
β-strand	91-93	3	6
β-strand	102	1	5
α-helix	109-124	16
β-strand	129-131	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spliceosomal U5 snRNP-specific 15 kDa protein	A, C, E	protein	142	Homo sapiens	P83876 (AlphaFold model)
CD2 antigen cytoplasmic tail-binding protein 2	B, D, F	protein	86	Homo sapiens	O95400 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>1SYX_1 Spliceosomal U5 snRNP-specific 15 kDa protein (chains A, C, E)
MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYL
VDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVY
RGARKGRGLVVSPKDYSTKYRY

Sequence of entity 2 (B, D, F), FASTA

>1SYX_2 CD2 antigen cytoplasmic tail-binding protein 2 (chains B, D, F)
AEEELETPTPTQRGEAESRGDGLVDVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPD
GVYCRKLDPPGGQFYNSKRIDFDLYT

Primary citation

Structural basis for the bifunctionality of the U5 snRNP 52K protein (CD2BP2). Nielsen, T.K., Liu, S., Luhrmann, R. et al. J Mol Biol (2007) 369:902-908. DOI 10.1016/j.jmb.2007.03.077 · PubMed

Other PDB entries of the same protein (UniProt P83876 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QGV 1.4 Å, Human spliceosomal protein U5-15KD
4BWQ 2.1 Å, Crystal structure of U5-15kD in a complex with PQBP1
4BWS 2.5 Å, Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD.
4CDO 2.5 Å, Crystal structure of PQBP1 bound to spliceosomal U5-15kD
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.
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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