9GCM: U11 snRNP core

Structure of the U11 snRNP core. Determined by electron microscopy at 3.1 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,466
Mol. weight: 143.1 kDa
Released: 5 Feb 2025

Explore 9GCM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GCM contains 15 α-helices and 16 β-strands across 3 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 B: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	15-17	3
α-helix	26-37	12
β-strand	40-46	7	1
β-strand	52-58	7	1
β-strand	62	1	2
α-helix	63-81	19
α-helix	89-95	7
β-strand	96-100	5	3
β-strand	103-104	2	3
β-strand	111	1	2
β-strand	121-123	3	1
β-strand	124-127	4	3

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
α-helix	29-36	8
α-helix	49-51	3
β-strand	52-56	5	4
α-helix	64-71	8
α-helix	72-74	3
β-strand	77-84	8	4
β-strand	91-99	9	4
α-helix	102-112	11
β-strand	116-117	2	5
β-strand	120-121	2	5
β-strand	123-124	2	4
β-strand	146-147	2	6
α-helix	148-150	3
β-strand	152-153	2	6

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	292-331	40
α-helix	333-336	4
α-helix	341-383	43

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
U11 snRNA	A	RNA	135	Homo sapiens
U11/U12 small nuclear ribonucleoprotein 25 kDa protein	B	protein	132	Homo sapiens	Q9BV90 (AlphaFold model)
U11/U12 small nuclear ribonucleoprotein 35 kDa protein	C	protein	246	Homo sapiens	Q16560 (AlphaFold model)
Programmed cell death protein 7	D	protein	485	Homo sapiens	Q8N8D1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9GCM_1 U11 snRNA (chains A)
AAAAAGGGCUUCUGUCGUGAGUGGCACACGUAGGGCAACUCGAUUGCUCUGCGUGCGGAA
UCGACAUCAAGAGAUUUCGGAAGCAUAAUUUUUUGGUAUUUGGGCAGCUGGUGAUCGUUG
GUCCCGGCGCCCUUU

Sequence of entity 2 (B), FASTA

>9GCM_2 U11/U12 small nuclear ribonucleoprotein 25 kDa protein (chains B)
MDVFQEGLAMVVQDPLLCDLPIQVTLEEVNSQIALEYGQAMTVRVCKMDGEVMPVVVVQS
ATVLDLKKAIQRYVQLKQEREGGIQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNR
DEVSFIKKLRQK

Sequence of entity 3 (C), FASTA

>9GCM_3 U11/U12 small nuclear ribonucleoprotein 35 kDa protein (chains C)
MNDWMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYVPNKGVIGDPLLTLFVARLNL
QTKEDKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERAVIKAYRDADGLVIDQH
EIFVDYELERTLKGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINLPVVKNDLYREGK
RERRERSRSRERHWDSRTRDRDHDRGREKRWQEREPTRVWPDNDWERERDFRDDRIKGRE
KKERGK

Sequence of entity 4 (D), FASTA

>9GCM_4 Programmed cell death protein 7 (chains D)
MALPPFFGQGRPGPPPPQPPPPAPFGCPPPPLPSPAFPPPLPQRPGPFPGASAPFLQPPL
ALQPRASAEASRGGGGAGAFYPVPPPPLPPPPPQCRPFPGTDAGERPRPPPPGPGPPWSP
RWPEAPPPPADVLGDAALQRLRDRQWLEAVFGTPRRAGCPVPQRTHAGPSLGEVRARLLR
ALRLVRRLRGLSQALREAEADGAAWVLLYSQTAPLRAELAERLQPLTQAAYVGEARRRLE
RVRRRRLRLRERAREREAEREAEAARAVEREQEIDRWRVKCVQEVEEKKREQELKAAADG
VLSEVRKKQADTKRMVDILRALEKLRKLRKEAAARKGVCPPASADETFTHHLQRLRKLIK
KRSELYEAEERALRVMLEGEQEEERKRELEKKQRKEKEKILLQKREIESKLFGDPDEFPL
AHLLEPFRQYYLQAEHSLPALIQIRHDWDQYLVPSDHPKGNFVPQGWVLPPLPSNDIWAT
AVKLH

Primary citation

Structural basis of 5' splice site recognition by the minor spliceosome. Zhao, J., Peter, D., Brandina, I. et al. Mol Cell (2025) 85:652. DOI 10.1016/j.molcel.2024.12.017 · PubMed

Other PDB entries of the same protein (UniProt Q9BV90 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Y6O 3.38 Å, Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11…
8R7N 3.4 Å, Overall structure of the U11 snRNP
9GBZ 3.4 Å, 5'-lobe of the substrate-bound U11 snRNP
9GBW 3.5 Å, Overall structure of the substrate-bound U11 snRNP

Browse structure collections

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