9GCL: U11 snRNP C-lobe

Structure of the U11 snRNP C-lobe. Determined by electron microscopy at 3.0 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 10
Atoms: 7,307
Mol. weight: 198.05 kDa
Released: 5 Feb 2025

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

Secondary structure: helices and β-sheets

9GCL contains 30 α-helices and 51 β-strands across 9 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 E: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	12-15	4	1
α-helix	18-25	8
α-helix	28-40	13

Chain F: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	56-57	2	5
β-strand	65-66	2	5
α-helix	68-82	15
α-helix	87-92	6
α-helix	96-100	5
β-strand	107-108	2	4
α-helix	112-126	15
α-helix	127-129	3
α-helix	134-137	4
α-helix	144-146	3
α-helix	149-155	7
α-helix	158-177	20
α-helix	237-253	17
α-helix	254-258	5
α-helix	259-267	9

Chain h: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
β-strand	14-19	6	2
β-strand	24-31	8	2
β-strand	39-46	8	2
β-strand	52-60	9	2
α-helix	62-64	3
β-strand	65-70	6	2
α-helix	76-79	4

Chain i: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
α-helix	30-37	8
β-strand	42-46	5	2
β-strand	51-59	9	2
β-strand	65-73	9	2
β-strand	74-76	3	6
β-strand	90-92	3	6
β-strand	95-101	7	2
α-helix	103-105	3
β-strand	106-111	6	2

Chain j: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	17	1	3
β-strand	19-22	4	2
β-strand	27-28	2	2
β-strand	31-35	5	3
β-strand	41-44	4	3
β-strand	48-49	2	2
β-strand	55-56	2	2
β-strand	60-63	4	3
α-helix	65-67	3
β-strand	68-72	5	2
α-helix	75-79	5

Chain k: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	16-21	6	2
β-strand	26-33	8	2
β-strand	41-50	10	2
β-strand	62-68	7	2
β-strand	70-72	3	2
α-helix	74-76	3
β-strand	77-82	6	2

Chain l: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	17-27	11
β-strand	31-34	4	2
α-helix	35	1
β-strand	42-45	4	2
β-strand	47	1	2
β-strand	58-65	8	2
β-strand	70-77	8	2
β-strand	86-88	3	2

Chain m: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-14	8
β-strand	18-23	6	2
β-strand	28	1	2
β-strand	30-36	7	2
β-strand	42-51	10	2
β-strand	54-64	11	2
β-strand	69-74	6	2

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Zinc finger matrin-type protein 5	E	protein	170	Homo sapiens	Q9UDW3 (AlphaFold model)
Small nuclear ribonucleoprotein Sm D1	h	protein	119	Homo sapiens	P62314 (AlphaFold model)
Small nuclear ribonucleoprotein Sm D3	j	protein	126	Homo sapiens	P62318 (AlphaFold model)
Small nuclear ribonucleoprotein-associated proteins B and B'	k	protein	240	Homo sapiens	P14678 (AlphaFold model)
Small nuclear ribonucleoprotein E	l	protein	92	Homo sapiens	P62304
Small nuclear ribonucleoprotein F	m	protein	86	Homo sapiens	P62306
Small nuclear ribonucleoprotein G	n	protein	76	Homo sapiens	P62308
U11/U12 small nuclear ribonucleoprotein 48 kDa protein	F	protein	339	Homo sapiens	Q6IEG0
Small nuclear ribonucleoprotein Sm D2	i	protein	118	Homo sapiens	P62316
U11 snRNA	A	RNA	135	Homo sapiens

Sequence of entity 1 (E), FASTA

>9GCL_1 Zinc finger matrin-type protein 5 (chains E)
MGKRYFCDYCDRSFQDNLHNRKKHLNGLQHLKAKKVWYDMFRDAAAILLDEQNKRPCRKF
LLTGQCDFGSNCRFSHMSERDLQELSIQVEEERRAREWLLDAPELPEGHLEDWLEKRAKR
LSSAPSSRAEPIRTTVFQYPVGWPPVQELPPSLRAPPPGGWPLQPRVQWG

Sequence of entity 2 (h), FASTA

>9GCL_2 Small nuclear ribonucleoprotein Sm D1 (chains h)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR

Sequence of entity 3 (j), FASTA

>9GCL_3 Small nuclear ribonucleoprotein Sm D3 (chains j)
MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ
VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGN
IFQKRR

Sequence of entity 4 (k), FASTA

>9GCL_4 Small nuclear ribonucleoprotein-associated proteins B and B' (chains k)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM
PQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMG
RGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGPPPPGMRPPRP

Sequence of entity 5 (l), FASTA

>9GCL_5 Small nuclear ribonucleoprotein E (chains l)
MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD
AEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN

Sequence of entity 6 (m), FASTA

>9GCL_6 Small nuclear ribonucleoprotein F (chains m)
MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG
EVLIRCNNVLYIRGVEEEEEDGEMRE

Sequence of entity 7 (n), FASTA

>9GCL_7 Small nuclear ribonucleoprotein G (chains n)
MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV
VIRGNSIIMLEALERV

Sequence of entity 8 (F), FASTA

>9GCL_8 U11/U12 small nuclear ribonucleoprotein 48 kDa protein (chains F)
MEGEPPPVEERRRLQEELNEFVESGCRTLEEVTASLGWDLDSLDPGEEEAAEDEVVICPY
DSNHHMPKSSLAKHMASCRLRKMGYTKEEEDEMYNPEFFYENVKIPSITLNKDSQFQIIK
QARTAVGKDSDCYNQRIYSSLPVEVPLNHKRFVCDLTQADRLALYDFVVEETKKKRSDSQ
IIENDSDLFVDLAAKINQDNSRKSPKSYLEILAEVRDYKRRRQSYRAKNVHITKKSYTEV
IRDVINVHMEELSNHWQEEQEKAEDDAEKNEERRSASVDSRQSGGSYLDAECSRHRRDRS
RSPHKRKRNKDKDKNCESRRRKERDGERHHSHKRRKQKI

Sequence of entity 9 (i), FASTA

>9GCL_9 Small nuclear ribonucleoprotein Sm D2 (chains i)
MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK

Sequence of entity 10 (A), FASTA

>9GCL_10 U11 snRNA (chains A)
AAAAAGGGCUUCUGUCGUGAGUGGCACACGUAGGGCAACUCGAUUGCUCUGCGUGCGGAA
UCGACAUCAAGGGCUUUCGGAAGCAUAAUUUUUUGGUAUUUGGGCAGCUGGUGAUCGUUG
GUCCCGGCGCCCUUU

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 Q9UDW3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GC0 3.2 Å, 3'-lobe of the substrate-bound U11 snRNP
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
9GBW 3.5 Å, Overall structure of the substrate-bound U11 snRNP

Browse structure collections

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