9NH5: Small nuclear ribonucleoprotein Sm D3
CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (core region). Determined by electron microscopy at 2.82 Å resolution. Released 21 Jan 2026.
- Method
- Electron microscopy
- Resolution
- 2.82 Å
- Organisms
- Homo sapiens, Trichoplusia ni
- Chains
- 13
- Atoms
- 16,094
- Mol. weight
- 438.22 kDa
- Ligands
- ZN
- Released
- 21 Jan 2026
Explore 9NH5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9NH5 contains 87 α-helices and 92 β-strands across 11 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: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-12 | 8 | |
| β-strand | 17-22 | 6 | 1 |
| β-strand | 27-35 | 9 | 1 |
| β-strand | 41-49 | 9 | 1 |
| β-strand | 55-63 | 9 | 1 |
| α-helix | 65-67 | 3 | |
| β-strand | 68-73 | 6 | 1 |
| α-helix | 75-79 | 5 | |
| α-helix | 81-83 | 3 | |
Chain B: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-12 | 4 | |
| β-strand | 16-21 | 6 | 1 |
| β-strand | 26-33 | 8 | 1 |
| β-strand | 40-48 | 9 | 1 |
| β-strand | 64-72 | 9 | 1 |
| α-helix | 74-76 | 3 | |
| β-strand | 77-84 | 8 | 1 |
Chain C: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-15 | 9 | |
| α-helix | 18-21 | 4 | |
| β-strand | 28-33 | 6 | 1 |
| β-strand | 38-46 | 9 | 1 |
| β-strand | 52-60 | 9 | 1 |
| β-strand | 66-74 | 9 | 1 |
| α-helix | 76-78 | 3 | |
| β-strand | 79-83 | 5 | 1 |
| α-helix | 90-106 | 17 | |
Chain D: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 108-114 | 7 | |
| α-helix | 148-150 | 3 | |
| α-helix | 155-164 | 10 | |
| β-strand | 168-174 | 7 | 1 |
| β-strand | 179-182 | 4 | 1 |
| β-strand | 185-188 | 4 | 1 |
| β-strand | 196-198 | 3 | 1 |
| β-strand | 201-206 | 6 | 1 |
| β-strand | 338-343 | 6 | 1 |
| β-strand | 346-348 | 3 | 1 |
| α-helix | 350-352 | 3 | |
| β-strand | 353-358 | 6 | 1 |
Chain E: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-27 | 11 | |
| β-strand | 30-35 | 6 | 1 |
| β-strand | 38-49 | 12 | 1 |
| β-strand | 56-65 | 10 | 1 |
| β-strand | 71-79 | 9 | 1 |
| α-helix | 81-83 | 3 | |
| β-strand | 84-89 | 6 | 1 |
Chain F: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-12 | 6 | |
| β-strand | 18-23 | 6 | 1 |
| β-strand | 27-35 | 9 | 1 |
| β-strand | 42-51 | 10 | 1 |
| β-strand | 54-58 | 5 | 1 |
| β-strand | 61-64 | 4 | 1 |
| α-helix | 66-68 | 3 | |
| β-strand | 69-74 | 6 | 1 |
Chain G: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-7 | 3 | |
| α-helix | 10-12 | 3 | |
| β-strand | 16-21 | 6 | 1 |
| α-helix | 22-24 | 3 | |
| β-strand | 26-34 | 9 | 1 |
| β-strand | 40-48 | 9 | 1 |
| β-strand | 54-62 | 9 | 1 |
| α-helix | 64-66 | 3 | |
| β-strand | 67-72 | 6 | 1 |
Chain H: 23 helices, 26 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-18 | 8 | 2 |
| β-strand | 27-32 | 6 | 2 |
| β-strand | 35-39 | 5 | 2 |
| α-helix | 49-52 | 4 | |
| α-helix | 56-58 | 3 | |
| α-helix | 61-63 | 3 | |
| β-strand | 66-68 | 3 | 2 |
| α-helix | 74-77 | 4 | |
| α-helix | 80-81 | 2 | |
| α-helix | 82-86 | 5 | |
| β-strand | 92-95 | 4 | 2 |
| α-helix | 97-113 | 17 | |
| α-helix | 125-131 | 7 | |
| α-helix | 132-134 | 3 | |
| β-strand | 135-137 | 3 | 2 |
| β-strand | 144-146 | 3 | 3 |
| β-strand | 149-155 | 7 | 3 |
| β-strand | 163-169 | 7 | 3 |
| β-strand | 172-178 | 7 | 3 |
| α-helix | 189-192 | 4 | |
| β-strand | 200-204 | 5 | 3 |
| α-helix | 216-231 | 16 | |
| β-strand | 235-237 | 3 | 4 |
| α-helix | 246-259 | 14 | |
| α-helix | 261-263 | 3 | |
| β-strand | 268-271 | 4 | 4 |
| α-helix | 273-284 | 12 | |
| α-helix | 286-288 | 3 | |
| α-helix | 291-294 | 4 | |
| β-strand | 308-310 | 3 | 4 |
| α-helix | 314-316 | 3 | |
| β-strand | 323-327 | 5 | 4 |
| α-helix | 335-344 | 10 | |
| β-strand | 351-354 | 4 | 4 |
| α-helix | 357-359 | 3 | |
| α-helix | 363-366 | 4 | |
| α-helix | 367-369 | 3 | |
| β-strand | 373-375 | 3 | 5 |
| β-strand | 381-383 | 3 | 5 |
| β-strand | 387-390 | 4 | 4 |
| α-helix | 399-409 | 11 | |
| β-strand | 413-417 | 5 | 3 |
| α-helix | 421-435 | 15 | |
| β-strand | 444-446 | 3 | 3 |
| β-strand | 454-457 | 4 | 2 |
| β-strand | 462-466 | 5 | 6 |
| β-strand | 480-481 | 2 | 7 |
| β-strand | 484-487 | 4 | 6 |
| β-strand | 492-495 | 4 | 6 |
3 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 |
|---|
| Small nuclear ribonucleoprotein Sm D3 | A | protein | 146 | Homo sapiens | P62318 (AlphaFold model) |
| Small nuclear ribonucleoprotein-associated proteins B and B' | B | protein | 95 | Homo sapiens | P14678 (AlphaFold model) |
| Small nuclear ribonucleoprotein F | F | protein | 86 | Homo sapiens | P62306 (AlphaFold model) |
| Small nuclear ribonucleoprotein E | E | protein | 92 | Homo sapiens | P62304 (AlphaFold model) |
| Small nuclear ribonucleoprotein G | G | protein | 84 | Homo sapiens | P62308 |
| U7 snRNA-associated Sm-like protein LSm10 | C | protein | 123 | Homo sapiens | Q969L4 |
| U7 snRNA-associated Sm-like protein LSm11 | D | protein | 371 | Homo sapiens | P83369 |
| Cleavage and polyadenylation specificity factor subunit 3 | H | protein | 684 | Homo sapiens | Q9UKF6 |
| Cleavage and polyadenylation specificity factor subunit 2 | I | protein | 782 | Homo sapiens | Q9P2I0 |
| Symplekin | J | protein | 1072 | Homo sapiens | Q92797 |
| Cleavage stimulation factor subunit 3 | K | protein | 8 | Trichoplusia ni | |
| U7 snRNA | Z | RNA | 64 | Homo sapiens | |
1 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>9NH5_1 Small nuclear ribonucleoprotein Sm D3 (chains A)
MGSSHHHHHHSSGLVPRGSHMSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMN
CQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKA
AILKAQVAARGRGRGMGRGNIFQKRR
Sequence of entity 2 (B), FASTA
>9NH5_2 Small nuclear ribonucleoprotein-associated proteins B and B' (chains B)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARV
Sequence of entity 3 (F), FASTA
>9NH5_3 Small nuclear ribonucleoprotein F (chains F)
MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG
EVLIRCNNVLYIRGVEEEEEDGEMRE
Sequence of entity 4 (E), FASTA
>9NH5_4 Small nuclear ribonucleoprotein E (chains E)
MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD
AEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN
Sequence of entity 5 (G), FASTA
>9NH5_5 Small nuclear ribonucleoprotein G (chains G)
MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV
VIRGNSIIMLEALERVLEHHHHHH
Sequence of entity 6 (C), FASTA
>9NH5_6 U7 snRNA-associated Sm-like protein LSm10 (chains C)
MAVSHSVKERTISENSLIILLQGLQGRVTTVDLRDESVAHGRIDNVDAFMNIRLAKVTYT
DRWGHQVKLDDLFVTGRNVRYVHIPDDVNITSTIEQQLQIIHRVRNFGGKGQGRWEFPPK
NCK
Sequence of entity 7 (D), FASTA
>9NH5_7 U7 snRNA-associated Sm-like protein LSm11 (chains D)
MHHHHHHSGGSMEERERGARSAGAGSPARPPSPRLDVSSDSFDPLLALYAPRLPPIPYPN
APCFNNVAEYESFLRTGVRGGGRGRGRARGAAAGSGVPAAPGPSGRTRRRPDAPAPDPER
IQRLRRLMVAKEEGDGAAGAGRRGPGRSRKAPRNVLTRMPLHEGSPLGELHRCIREGVKV
NVHIRTFKGLRGVCTGFLVAFDKFWNMALTDVDETYRKPVLGKAYERDSSLTLTRLFDRL
KLQDSSKKEADSKSAVEDSTLSRYSQTSTWKLASVWGRADTGRGSHKRSRSVPSSLQASA
REESRSELSGRTTRTDGSSVGGTFSRATTLSRGQSRKKKRKPKVDYQQVFTRHINQIFIR
GENVLLVHLAQ
Sequence of entity 8 (H), FASTA
>9NH5_8 Cleavage and polyadenylation specificity factor subunit 3 (chains H)
MSAIPAEESDQLLIRPLGAGQEVGRSCIILEFKGRKIMLDCGIHPGLEGMDALPYIDLID
PAEIDLLLISHFHLDHCGALPWFLQKTSFKGRTFMTHATKAIYRWLLSDYVKVSNISADD
MLYTETDLEESMDKIETINFHEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDF
SRQEDRHLMAAEIPNIKPDILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPV
FALGRAQELLLILDEYWQNHPELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQININ
NPFVFKHISNLKSMDHFDDIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVE
GTLAKHIMSEPEEITTMSGQKLPLKMSVDYISFSAHTDYQQTSEFIRALKPPHVILVHGE
QNEMARLKAALIREYEDNDEVHIEVHNPRNTEAVTLNFRGEKLAKVMGFLADKKPEQGQR
VSGILVKRNFNYHILSPCDLSNYTDLAMSTVKQTQAIPYTGPFNLLCYQLQKLTGDVEEL
EIQEKPALKVFKNITVIQEPGMVVLEWLANPSNDMYADTVTTVILEVQSNPKIRKGAVQK
VSKKLEMHVYSKRLEIMLQDIFGEDCVSVKDDSILSVTVDGKTANLNLETRTVECEEGSE
DDESLREMVELAAQRLYEALTPVH
Sequence of entity 9 (I), FASTA
>9NH5_9 Cleavage and polyadenylation specificity factor subunit 2 (chains I)
MTSIIKLTTLSGVQEESALCYLLQVDEFRFLLDCGWDEHFSMDIIDSLRKHVHQIDAVLL
SHPDPLHLGALPYAVGKLGLNCAIYATIPVYKMGQMFMYDLYQSRHNTEDFTLFTLDDVD
AAFDKIQQLKFSQIVNLKGKGHGLSITPLPAGHMIGGTIWKIVKDGEEEIVYAVDFNHKR
EIHLNGCSLEMLSRPSLLITDSFNATYVQPRRKQRDEQLLTNVLETLRGDGNVLIAVDTA
GRVLELAQLLDQIWRTKDAGLGVYSLALLNNVSYNVVEFSKSQVEWMSDKLMRCFEDKRN
NPFQFRHLSLCHGLSDLARVPSPKVVLASQPDLECGFSRDLFIQWCQDPKNSIILTYRTT
PGTLARFLIDNPSEKITEIELRKRVKLEGKELEEYLEKEKLKKEAAKKLEQSKEADIDSS
DESDIEEDIDQPSAHKTKHDLMMKGEGSRKGSFFKQAKKSYPMFPAPEERIKWDEYGEII
KPEDFLVPELQATEEEKSKLESGLTNGDEPMDQDLSDVPTKCISTTESIEIKARVTYIDY
EGRSDGDSIKKIINQMKPRQLIIVHGPPEASQDLAECCRAFGGKDIKVYMPKLHETVDAT
SETHIYQVRLKDSLVSSLQFCKAKDAELAWIDGVLDMRVSKVDTGVILEEGELKDDGEDS
EMQVEAPSDSSVIAQQKAMKSLFGDDEKETGEESEIIPTLEPLPPHEVPGHQSVFMNEPR
LSDFKQVLLREGIQAEFVGGVLVCNNQVAVRRTETGRIGLEGCLCQDFYRIRDLLYEQYA
IV
Sequence of entity 10 (J), FASTA
>9NH5_10 Symplekin (chains J)
MTTSERVVDLLNQAALITNDSKITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVR
KFVIGFIEEACKRDIELLLKLIANLNMLLRDENVNVVKKAILTMTQLYKVALQWMVKSRV
ISELQEACWDMVSAMAGDIILLLDSDNDGIRTHAIKFVEGLIVTLSPRMADSEIPRRQEH
DISLDRIPRDHPYIQYNVLWEEGKAALEQLLKFMVHPAISSINLTTALGSLANIARQRPM
FMSEVIQAYETLHANLPPTLAKSQVSSVRKNLKLHLLSVLKHPASLEFQAQITTLLVDLG
TPQAEIARNMPSSKDTRKRPRDDSDSTLKKMKLEPNLGEDDEDKDLEPGPSGTSKASAQI
SGQSDTDITAEFLQPLLTPDNVANLVLISMVYLPEAMPASFQAIYTPVESAGTEAQIKHL
ARLMATQMTAAGLGPGVEQTKQCKEEPKEEKVVKTESVLIKRRLSAQGQAISVVGSLSSM
SPLEEEAPQAKRRPEPIIPVTQPRLAGAGGRKKIFRLSDVLKPLTDAQVEAMKLGAVKRI
LRAEKAVACSGAAQVRIKILASLVTQFNSGLKAEVLSFILEDVRARLDLAFAWLYQEYNA
YLAAGASGSLDKYEDCLIRLLSGLQEKPDQKDGIFTKVVLEAPLITESALEVVRKYCEDE
SRTYLGMSTLRDLIFKRPSRQFQYLHVLLDLSSHEKDKVRSQALLFIKRMYEKEQLREYV
EKFALNYLQLLVHPNPPSVLFGADKDTEVAAPWTEETVKQCLYLYLALLPQNHKLIHELA
AVYTEAIADIKRTVLRVIEQPIRGMGMNSPELLLLVENCPKGAETLVTRCLHSLTDKVPP
SPELVKRVRDLYHKRLPDVRFLIPVLNGLEKKEVIQALPKLIKLNPIVVKEVFNRLLGTQ
HGEGNSALSPLNPGELLIALHNIDSVKCDMKSIIKATNLCFAERNVYTSEVLAVVMQQLM
EQSPLPMLLMRTVIQSLTMYPRLGGFVMNILSRLIMKQVWKYPKVWEGFIKCCQRTKPQS
FQVILQLPPQQLGAVFDKCPELREPLLAHVRSFTPHQQAHIPNSIMTILEAS
Sequence of entity 11 (K), FASTA
>9NH5_11 Cleavage stimulation factor subunit 3 (chains K)
NDIYRQRQ
Sequence of entity 12 (Z), FASTA
>9NH5_12 U7 snRNA (chains Z)
GCAGUGUUACAGCUCUUUUAGAAUUUGUCUAGUAGGCUUUCUGGCUUUUUACCGGAAAGC
CCCU
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
An N-terminal helix of Lsm11 stabilizes CPSF73 in U7 snRNP for histone pre-mRNA 3'-end processing. Desotell, A., Marzluff, W.F., Dominski, Z. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkaf1442 · PubMed
Other PDB entries of the same protein (UniProt P62318 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3VRI 1.6 Å, HLA-B*57:01-RVAQLENVYI in complex with abacavir
- 1D3B 2.0 Å, Crystal structure of the D3B subcomplex of the human core snrnp domain at 2.0A resolution
- 9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
- 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
- 9NH6 2.82 Å, cryo-EM structure of human U7 snrnp with methylated noncleavable H2A* substrate pre-mRNA…
- 6ID1 2.86 Å, Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex)…
- 7DVQ 2.89 Å, Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)
- 6ID0 2.9 Å, Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1…
Browse structure collections
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