9GBW: PDB entry 9GBW
Overall structure of the substrate-bound U11 snRNP. Determined by electron microscopy at 3.5 Å resolution. Released 5 Feb 2025.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Homo sapiens
- Chains
- 14
- Atoms
- 13,570
- Mol. weight
- 301.02 kDa
- Released
- 5 Feb 2025
Explore 9GBW in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9GBW contains 49 α-helices and 70 β-strands across 12 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 | 4-12 | 9 | |
| 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 | 97-99 | 3 | 3 |
| β-strand | 104-105 | 2 | 3 |
| β-strand | 111 | 1 | 2 |
| β-strand | 122-123 | 2 | 1 |
| β-strand | 124-126 | 3 | 3 |
Chain C: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-17 | 3 | |
| α-helix | 30-36 | 7 | |
| β-strand | 52-56 | 5 | 4 |
| α-helix | 64-72 | 9 | |
| β-strand | 80-84 | 5 | 4 |
| β-strand | 91-98 | 8 | 4 |
| α-helix | 104-110 | 7 | |
| β-strand | 118 | 1 | 5 |
| β-strand | 120 | 1 | 5 |
| β-strand | 123-126 | 4 | 4 |
| α-helix | 138-140 | 3 | |
| β-strand | 145 | 1 | 6 |
| β-strand | 154 | 1 | 6 |
Chain D: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 172-197 | 26 | |
| α-helix | 202-223 | 22 | |
| α-helix | 224-228 | 5 | |
| α-helix | 234-278 | 45 | |
| α-helix | 279-283 | 5 | |
| α-helix | 284-335 | 52 | |
| α-helix | 341-390 | 50 | |
Chain E: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-7 | 3 | 7 |
| β-strand | 12-14 | 3 | 7 |
| α-helix | 18-24 | 7 | |
| α-helix | 28-40 | 13 | |
Chain F: 13 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-31 | 24 | |
| β-strand | 56-57 | 2 | 13 |
| β-strand | 65-66 | 2 | 13 |
| α-helix | 71-82 | 12 | |
| α-helix | 87-92 | 6 | |
| α-helix | 96-100 | 5 | |
| β-strand | 107-109 | 3 | 12 |
| α-helix | 112-129 | 18 | |
| α-helix | 132-136 | 5 | |
| α-helix | 144-146 | 3 | |
| α-helix | 149-155 | 7 | |
| α-helix | 158-177 | 20 | |
| α-helix | 222-224 | 3 | |
| α-helix | 231-234 | 4 | |
| α-helix | 237-256 | 20 | |
Chain h: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| β-strand | 14-19 | 6 | 8 |
| β-strand | 24-28 | 5 | 8 |
| β-strand | 29-31 | 3 | 9 |
| β-strand | 39-40 | 2 | 9 |
| β-strand | 43-46 | 4 | 8 |
| β-strand | 53-55 | 3 | 8 |
| β-strand | 59-60 | 2 | 9 |
| β-strand | 65-70 | 6 | 8 |
| α-helix | 76-81 | 6 | |
Chain i: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-17 | 3 | |
| α-helix | 20-26 | 7 | |
| α-helix | 30-38 | 9 | |
| β-strand | 42-46 | 5 | 8 |
| β-strand | 51-59 | 9 | 8 |
| β-strand | 65-76 | 12 | 8 |
| β-strand | 90-101 | 12 | 8 |
| α-helix | 103-105 | 3 | |
| β-strand | 106-111 | 6 | 8 |
Chain j: 4 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-12 | 8 | |
| β-strand | 17 | 1 | 10 |
| β-strand | 19-22 | 4 | 9 |
| β-strand | 27-28 | 2 | 9 |
| α-helix | 30 | 1 | |
| β-strand | 31-35 | 5 | 10 |
| β-strand | 41-44 | 4 | 10 |
| β-strand | 48-49 | 2 | 9 |
| β-strand | 55-56 | 2 | 9 |
| β-strand | 61-63 | 3 | 10 |
| α-helix | 65-67 | 3 | |
| β-strand | 68-72 | 5 | 9 |
| α-helix | 75-79 | 5 | |
4 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 |
|---|
| 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) |
| Zinc finger matrin-type protein 5 | E | protein | 170 | Homo sapiens | Q9UDW3 (AlphaFold model) |
| P120-5'SS | G | RNA | 11 | Homo sapiens | |
| Small nuclear ribonucleoprotein Sm D1 | h | protein | 119 | Homo sapiens | P62314 |
| Small nuclear ribonucleoprotein Sm D3 | j | protein | 126 | Homo sapiens | P62318 |
| Small nuclear ribonucleoprotein-associated proteins B and B' | k | protein | 240 | Homo sapiens | P14678 |
| 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 |
2 more molecules are not listed.
Sequence of entity 1 (B), FASTA
>9GBW_1 U11/U12 small nuclear ribonucleoprotein 25 kDa protein (chains B)
MDVFQEGLAMVVQDPLLCDLPIQVTLEEVNSQIALEYGQAMTVRVCKMDGEVMPVVVVQS
ATVLDLKKAIQRYVQLKQEREGGIQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNR
DEVSFIKKLRQK
Sequence of entity 2 (C), FASTA
>9GBW_2 U11/U12 small nuclear ribonucleoprotein 35 kDa protein (chains C)
MNDWMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYVPNKGVIGDPLLTLFVARLNL
QTKEDKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERAVIKAYRDADGLVIDQH
EIFVDYELERTLKGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINLPVVKNDLYREGK
RERRERSRSRERHWDSRTRDRDHDRGREKRWQEREPTRVWPDNDWERERDFRDDRIKGRE
KKERGK
Sequence of entity 3 (D), FASTA
>9GBW_3 Programmed cell death protein 7 (chains D)
MALPPFFGQGRPGPPPPQPPPPAPFGCPPPPLPSPAFPPPLPQRPGPFPGASAPFLQPPL
ALQPRASAEASRGGGGAGAFYPVPPPPLPPPPPQCRPFPGTDAGERPRPPPPGPGPPWSP
RWPEAPPPPADVLGDAALQRLRDRQWLEAVFGTPRRAGCPVPQRTHAGPSLGEVRARLLR
ALRLVRRLRGLSQALREAEADGAAWVLLYSQTAPLRAELAERLQPLTQAAYVGEARRRLE
RVRRRRLRLRERAREREAEREAEAARAVEREQEIDRWRVKCVQEVEEKKREQELKAAADG
VLSEVRKKQADTKRMVDILRALEKLRKLRKEAAARKGVCPPASADETFTHHLQRLRKLIK
KRSELYEAEERALRVMLEGEQEEERKRELEKKQRKEKEKILLQKREIESKLFGDPDEFPL
AHLLEPFRQYYLQAEHSLPALIQIRHDWDQYLVPSDHPKGNFVPQGWVLPPLPSNDIWAT
AVKLH
Sequence of entity 4 (E), FASTA
>9GBW_4 Zinc finger matrin-type protein 5 (chains E)
MGKRYFCDYCDRSFQDNLHNRKKHLNGLQHLKAKKVWYDMFRDAAAILLDEQNKRPCRKF
LLTGQCDFGSNCRFSHMSERDLQELSIQVEEERRAREWLLDAPELPEGHLEDWLEKRAKR
LSSAPSSRAEPIRTTVFQYPVGWPPVQELPPSLRAPPPGGWPLQPRVQWG
Sequence of entity 5 (G), FASTA
>9GBW_5 P120-5'SS (chains G)
AUAUCCUUUUU
Sequence of entity 6 (h), FASTA
>9GBW_6 Small nuclear ribonucleoprotein Sm D1 (chains h)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
Sequence of entity 7 (j), FASTA
>9GBW_7 Small nuclear ribonucleoprotein Sm D3 (chains j)
MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ
VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGN
IFQKRR
Sequence of entity 8 (k), FASTA
>9GBW_8 Small nuclear ribonucleoprotein-associated proteins B and B' (chains k)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM
PQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMG
RGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGPPPPGMRPPRP
Sequence of entity 9 (l), FASTA
>9GBW_9 Small nuclear ribonucleoprotein E (chains l)
MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD
AEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN
Sequence of entity 10 (m), FASTA
>9GBW_10 Small nuclear ribonucleoprotein F (chains m)
MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG
EVLIRCNNVLYIRGVEEEEEDGEMRE
Sequence of entity 11 (n), FASTA
>9GBW_11 Small nuclear ribonucleoprotein G (chains n)
MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV
VIRGNSIIMLEALERV
Sequence of entity 12 (F), FASTA
>9GBW_12 U11/U12 small nuclear ribonucleoprotein 48 kDa protein (chains F)
MEGEPPPVEERRRLQEELNEFVESGCRTLEEVTASLGWDLDSLDPGEEEAAEDEVVICPY
DSNHHMPKSSLAKHMASCRLRKMGYTKEEEDEMYNPEFFYENVKIPSITLNKDSQFQIIK
QARTAVGKDSDCYNQRIYSSLPVEVPLNHKRFVCDLTQADRLALYDFVVEETKKKRSDSQ
IIENDSDLFVDLAAKINQDNSRKSPKSYLEILAEVRDYKRRRQSYRAKNVHITKKSYTEV
IRDVINVHMEELSNHWQEEQEKAEDDAEKNEERRSASVDSRQSGGSYLDAECSRHRRDRS
RSPHKRKRNKDKDKNCESRRRKERDGERHHSHKRRKQKI
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:
- 9GCM 3.1 Å, Structure of the U11 snRNP core
- 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
Browse structure collections
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