1A9N: Spliceosomal U2B''-U2A' protein complex

Crystal structure of the spliceosomal U2B''-U2A' protein complex bound to a fragment of U2 small nuclear RNA. Determined by X-ray diffraction at 2.38 Å resolution. Released 23 Sept 1998.

Method: X-ray diffraction
Resolution: 2.38 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,188
Mol. weight: 78 kDa
Released: 23 Sept 1998

Explore 1A9N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1A9N contains 22 α-helices and 32 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
β-strand	14-16	3	1
β-strand	22-25	4	1
α-helix	37-40	4
β-strand	46-48	3	1
β-strand	56-57	2	2
β-strand	68-70	3	1
β-strand	78-79	2	2
α-helix	83-86	4
β-strand	92-94	3	1
α-helix	103-111	9
β-strand	117-119	3	1
α-helix	124-127	4
α-helix	131-138	8
β-strand	144-145	2	1
β-strand	148-149	2	1
α-helix	150-151	2
α-helix	152-160	9

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	5
α-helix	23-35	13
β-strand	40-44	5	5
β-strand	55-59	5	5
α-helix	62-71	10
β-strand	76-77	2	6
β-strand	80-81	2	6
β-strand	83-86	4	5
α-helix	92-98	7

Chain C: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
β-strand	14-16	3	3
β-strand	22-25	4	3
α-helix	37-40	4
β-strand	46-48	3	3
β-strand	56-57	2	4
β-strand	68-70	3	3
β-strand	78-79	2	4
α-helix	83-86	4
β-strand	92-94	3	3
α-helix	103-111	9
β-strand	117-119	3	3
α-helix	124-127	4
α-helix	131-138	8
β-strand	144-145	2	3
β-strand	148-149	2	3
α-helix	152-160	9
α-helix	165-172	8

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	7
α-helix	23-35	13
β-strand	40-44	5	7
β-strand	55-59	5	7
α-helix	62-72	11
β-strand	76-77	2	8
β-strand	80-81	2	8
β-strand	83-86	4	7
α-helix	92-97	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA (5'-r(cpcpupgpgpupapupupgpcpapgpupapcpcpupcpcpapgp* gp*u)-3')	Q, R	RNA	24	Homo sapiens
U2A'	A, C	protein	176	Homo sapiens	P09661 (AlphaFold model)
Spliceosomal U2B''	B, D	protein	96	Homo sapiens	P08579 (AlphaFold model)

Sequence of entity 1 (Q, R), FASTA

>1A9N_1 RNA (5'-R(*CP*CP*UP*GP*GP*UP*AP*UP*UP*GP*CP*AP*GP*UP*AP*CP*CP*UP*CP*CP*AP*GP* GP*U)-3') (chains Q, R)
CCUGGUAUUGCAGUACCUCCAGGU

Sequence of entity 2 (A, C), FASTA

>1A9N_2 U2A' (chains A, C)
MVKLTAELIEQAAQYTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGF
PLLRRLKTLLVNNNRICRIGEGLDQALPDLTELILTNNSLVELGDLDPLASLKSLTYLCI
LRNPVTNKKHYRLYVIYKVPQVRVLDFQKVKLKERQEAEKMFKGKRGAQLAKDIAR

Sequence of entity 3 (B, D), FASTA

>1A9N_3 SPLICEOSOMAL U2B'' (chains B, D)
MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG
SSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRG

Primary citation

Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA. Price, S.R., Evans, P.R., Nagai, K. Nature (1998) 394:645-650. DOI 10.1038/29234 · PubMed

Other PDB entries of the same protein (UniProt P09661 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
8C6J 2.8 Å, Human spliceosomal PM5 C* complex
6ID1 2.86 Å, Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex)…
6ID0 2.9 Å, Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1…
6ICZ 3.0 Å, Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom
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
8I0V 3.0 Å, The cryo-EM structure of human post-Bact complex

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