8Y6O
Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and tri-snRNP part
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A | pre-mRNA | polymer | 280 | 89522.7 | 1 | Homo sapiens (human) | ||
| 2 | B | U5 snRNA | polymer | 117 | 37254.9 | 1 | GenBank (20330981) | Homo sapiens (human) | |
| 3 | C | Pre-mRNA-processing-splicing factor 8 | polymer | 2335 | 273974.3 | 1 | UniProt (Q6P2Q9) Pfam (PF08082) Pfam (PF08083) Pfam (PF10598) Pfam (PF10597) Pfam (PF10596) Pfam (PF12134) Pfam (PF01398) Pfam (PF08084) In PDB | Homo sapiens (human) | 220 kDa U5 snRNP-specific protein,PRP8 homolog,Splicing factor Prp8,p220 |
| 4 | D | 116 kDa U5 small nuclear ribonucleoprotein component | polymer | 972 | 109560.6 | 1 | UniProt (Q15029) Pfam (PF00009) Pfam (PF03144) Pfam (PF14492) Pfam (PF03764) Pfam (PF00679) Pfam (PF16004) In PDB | Homo sapiens (human) | Elongation factor Tu GTP-binding domain-containing protein 2,SNU114 homolog,hSNU114,U5 snRNP-specific protein,116 kDa,U5-116 kDa |
| 5 | E | U5 small nuclear ribonucleoprotein 200 kDa helicase | polymer | 2136 | 244823.4 | 1 | UniProt (O75643) Pfam (PF21188) Pfam (PF18149) Pfam (PF00270) Pfam (PF00271) Pfam (PF02889) In PDB | Homo sapiens (human) | Activating signal cointegrator 1 complex subunit 3-like 1,BRR2 homolog,U5 snRNP-specific 200 kDa protein,U5-200KD |
| 6 | F | U5 small nuclear ribonucleoprotein 40 kDa protein | polymer | 357 | 39359.5 | 1 | UniProt (Q96DI7) Pfam (PF00400) In PDB | Homo sapiens (human) | U5 snRNP 40 kDa protein,U5-40K,38 kDa-splicing factor,Prp8-binding protein,hPRP8BP,U5 snRNP-specific 40 kDa protein,WD repeat-containing protein 57 |
| 7 | G | Pre-mRNA-processing factor 6 | polymer | 941 | 107092.2 | 1 | UniProt (O94906) Pfam (PF06424) Pfam (PF14559) Pfam (PF13432) In PDB | Homo sapiens (human) | Androgen receptor N-terminal domain-transactivating protein 1,ANT-1,PRP6 homolog,U5 snRNP-associated 102 kDa protein,U5-102 kDa protein |
| 8 | H | Thioredoxin-like protein 4B | polymer | 149 | 17034.6 | 1 | UniProt (Q9NX01) Pfam (PF02966) In PDB | Homo sapiens (human) | Dim1-like protein |
| 9 | I | Probable ATP-dependent RNA helicase DDX23 | polymer | 820 | 95785.1 | 1 | UniProt (Q9BUQ8) Pfam (PF00270) Pfam (PF00271) In PDB | Homo sapiens (human) | 100 kDa U5 snRNP-specific protein,DEAD box protein 23,PRP28 homolog,U5-100kD |
| 10 | a, h, o | Small nuclear ribonucleoprotein-associated proteins B and B' | polymer | 240 | 24642.1 | 3 | UniProt (P14678) Pfam (PF01423) In PDB | Homo sapiens (human) | snRNP-B,Sm protein B/B',Sm-B/B',SmB/B' |
| 11 | b, i, p | Small nuclear ribonucleoprotein Sm D1 | polymer | 119 | 13310.7 | 3 | UniProt (P62314) Pfam (PF01423) In PDB | Homo sapiens (human) | Sm-D1,Sm-D autoantigen,snRNP core protein D1 |
| 12 | c, j, q | Small nuclear ribonucleoprotein Sm D2 | polymer | 118 | 13551.9 | 3 | UniProt (P62316) Pfam (PF01423) In PDB | Homo sapiens (human) | Sm-D2,snRNP core protein D2 |
| 13 | d, k, r | Small nuclear ribonucleoprotein Sm D3 | polymer | 126 | 13940.3 | 3 | UniProt (P62318) Pfam (PF01423) In PDB | Homo sapiens (human) | Sm-D3,snRNP core protein D3 |
| 14 | e, l, s | Small nuclear ribonucleoprotein E | polymer | 92 | 10817.6 | 3 | UniProt (P62304) Pfam (PF01423) In PDB | Homo sapiens (human) | snRNP-E,Sm protein E,Sm-E,SmE |
| 15 | f, m, t | Small nuclear ribonucleoprotein F | polymer | 86 | 9734.2 | 3 | UniProt (P62306) Pfam (PF01423) In PDB | Homo sapiens (human) | snRNP-F,Sm protein F,Sm-F,SmF |
| 16 | g, n, u | Small nuclear ribonucleoprotein G | polymer | 76 | 8508.1 | 3 | UniProt (P62308) Pfam (PF01423) In PDB | Homo sapiens (human) | snRNP-G,Sm protein G,Sm-G,SmG |
| 17 | J | U4atac snRNA | polymer | 131 | 42049.8 | 1 | Homo sapiens (human) | ||
| 18 | K | U6atac snRNA | polymer | 125 | 40221.8 | 1 | GenBank (187960111) | Homo sapiens (human) | |
| 19 | L | U4/U6 small nuclear ribonucleoprotein Prp31 | polymer | 499 | 55529.0 | 1 | UniProt (Q8WWY3) Pfam (PF01798) Pfam (PF09785) In PDB | Homo sapiens (human) | Pre-mRNA-processing factor 31,Serologically defined breast cancer antigen NY-BR-99,U4/U6 snRNP 61 kDa protein,Protein 61K,hPrp31 |
| 20 | M | U4/U6 small nuclear ribonucleoprotein Prp4 | polymer | 522 | 58536.1 | 1 | UniProt (O43172) Pfam (PF08799) Pfam (PF00400) In PDB | Homo sapiens (human) | PRP4 homolog,hPrp4,U4/U6 snRNP 60 kDa protein,WD splicing factor Prp4 |
| 21 | N | U4/U6 small nuclear ribonucleoprotein Prp3 | polymer | 683 | 77669.2 | 1 | UniProt (O43395) Pfam (PF01480) Pfam (PF08572) Pfam (PF06544) In PDB | Homo sapiens (human) | Pre-mRNA-splicing factor 3,hPrp3,U4/U6 snRNP 90 kDa protein |
| 22 | O | NHP2-like protein 1 | polymer | 128 | 14191.5 | 1 | UniProt (P55769) Pfam (PF01248) In PDB | Homo sapiens (human) | High mobility group-like nuclear protein 2 homolog 1,OTK27,SNU13 homolog,hSNU13,U4/U6.U5 small nuclear ribonucleoprotein SNU13,U4/U6.U5 tri-snRNP 15.5 kDa protein |
| 23 | R | Centrosomal AT-AC splicing factor | polymer | 332 | 38034.2 | 1 | UniProt (Q86UT8) Pfam (PF14968) In PDB | Homo sapiens (human) | Coiled-coil domain-containing protein 84 |
| 24 | P | U11 snRNA | polymer | 135 | 43505.6 | 1 | GenBank (161169046) | Homo sapiens (human) | |
| 25 | V | Zinc finger matrin-type protein 5 | polymer | 170 | 20002.8 | 1 | UniProt (Q9UDW3) Pfam (PF06220) Pfam (PF00642) In PDB | Homo sapiens (human) | U11/U12 small nuclear ribonucleoprotein 20 kDa protein,U11/U12 snRNP 20 kDa protein,U11/U12-20K |
| 26 | W | U11/U12 small nuclear ribonucleoprotein 35 kDa protein | polymer | 246 | 29514.5 | 1 | UniProt (Q16560) Pfam (PF00076) In PDB | Homo sapiens (human) | U11/U12 snRNP 35 kDa protein,U11/U12-35K,Protein HM-1,U1 snRNP-binding protein homolog |
| 27 | X | U11/U12 small nuclear ribonucleoprotein 25 kDa protein | polymer | 132 | 15290.7 | 1 | UniProt (Q9BV90) Pfam (PF18036) In PDB | Homo sapiens (human) | U11/U12 snRNP 25 kDa protein,U11/U12-25K,Minus-99 protein |
| 28 | Y | U11/U12 small nuclear ribonucleoprotein 48 kDa protein | polymer | 339 | 40042.6 | 1 | UniProt (Q6IEG0) Pfam (PF05253) In PDB | Homo sapiens (human) | U11/U12 snRNP 48 kDa protein,U11/U12-48K |
| 29 | Z | Programmed cell death protein 7 | polymer | 485 | 54792.0 | 1 | UniProt (Q8N8D1) Pfam (PF16021) In PDB | Homo sapiens (human) | ES18,hES18 |
| 30 | S | U4/U6.U5 tri-snRNP-associated protein 1 | polymer | 800 | 90414.1 | 1 | UniProt (O43290) Pfam (PF19252) Pfam (PF03343) In PDB | Homo sapiens (human) | SNU66 homolog,hSnu66,Squamous cell carcinoma antigen recognized by T-cells 1,SART-1,hSART-1,U4/U6.U5 tri-snRNP-associated 110 kDa protein |
| 31 | U | U4/U6.U5 tri-snRNP-associated protein 2 | polymer | 565 | 65481.4 | 1 | UniProt (Q53GS9) Pfam (PF02148) Pfam (PF00443) In PDB | Homo sapiens (human) | Inactive ubiquitin-specific peptidase 39,SAD1 homolog,U4/U6.U5 tri-snRNP-associated 65 kDa protein,65K |
| 32 | Q | Serine/threonine-protein kinase PRP4 homolog | polymer | 1007 | 117265.0 | 1 | UniProt (Q13523) Pfam (PF00069) In PDB | Homo sapiens (human) | PRP4 kinase,PRP4 pre-mRNA-processing factor 4 homolog |
| 33 | B, D | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) | |||
| 34 | C | INOSITOL HEXAKISPHOSPHATE | non-polymer | 660.0 | 1 | Chemie (IHP) | |||
| 35 | D | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 1 | Chemie (GTP) | |||
| 36 | V, Y, U, R | ZINC ION | non-polymer | 65.4 | 6 | Chemie (ZN) |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 46 |
| Total formula weight | 2100462.3 | |
| Non-Polymers* | Number of molecules | 10 |
| Total formula weight | 1624.3 | |
| All* | Total formula weight | 2102086.5 |
