5O9Z
Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex)
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-processing-splicing factor 8 | polymer | 2335 | 273974.3 | 1 | UniProt (Q6P2Q9) Pfam (PF08084) Pfam (PF08082) Pfam (PF08083) Pfam (PF10598) Pfam (PF10597) Pfam (PF10596) Pfam (PF12134) Pfam (PF01398) In PDB | Homo sapiens (Human) | 220 kDa U5 snRNP-specific protein,PRP8 homolog,Splicing factor Prp8,p220 |
| 2 | B | 116 kDa U5 small nuclear ribonucleoprotein component | polymer | 972 | 109560.6 | 1 | UniProt (Q15029) Pfam (PF16004) Pfam (PF00009) Pfam (PF03144) Pfam (PF14492) Pfam (PF03764) Pfam (PF00679) 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 |
| 3 | C | 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 |
| 4 | D | U5 small nuclear ribonucleoprotein 40 kDa protein | polymer | 357 | 39359.5 | 1 | UniProt (Q96DI7) Pfam (PF00400) In PDB | Homo sapiens (Human) | U5-40K,38 kDa-splicing factor,Prp8-binding protein,hPRP8BP,U5 snRNP-specific 40 kDa protein,WD repeat-containing protein 57 |
| 5 | E | 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 |
| 6 | F | U4/U6 small nuclear ribonucleoprotein Prp4 | polymer | 521 | 58408.0 | 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 |
| 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 | 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,hPrp31 |
| 9 | I | Pre-mRNA-splicing factor 38A | polymer | 312 | 37563.9 | 1 | UniProt (Q8NAV1) Pfam (PF03371) Pfam (PF12871) In PDB | Homo sapiens (Human) | |
| 10 | J | Thioredoxin-like protein 4A | polymer | 142 | 16807.3 | 1 | UniProt (P83876) Pfam (PF02966) In PDB | Homo sapiens (Human) | DIM1 protein homolog,Spliceosomal U5 snRNP-specific 15 kDa protein,Thioredoxin-like U5 snRNP protein U5-15kD |
| 11 | K | Microfibrillar-associated protein 1 | polymer | 439 | 52050.5 | 1 | UniProt (P55081) Pfam (PF06991) In PDB | Homo sapiens (Human) | |
| 12 | L | WD40 repeat-containing protein SMU1 | polymer | 513 | 57616.7 | 1 | UniProt (Q2TAY7) Pfam (PF17814) Pfam (PF00400) In PDB | Homo sapiens (Human) | Smu-1 suppressor of mec-8 and unc-52 protein homolog |
| 13 | M | Peptidyl-prolyl cis-trans isomerase H | polymer | 177 | 19230.1 | 1 | UniProt (O43447) Pfam (PF00160) In PDB | Homo sapiens (Human) | PPIase H,Rotamase H,Small nuclear ribonucleoprotein particle-specific cyclophilin H,CypH,U-snRNP-associated cyclophilin SnuCyp-20,USA-CYP |
| 14 | N | Zinc finger matrin-type protein 2 | polymer | 199 | 23664.0 | 1 | UniProt (Q96NC0) Pfam (PF12171) In PDB | Homo sapiens (Human) | |
| 15 | 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 |
| 16 | P | 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,hSART-1,U4/U6.U5 tri-snRNP-associated 110 kDa protein |
| 17 | Q | WW domain-binding protein 4 | polymer | 376 | 42575.8 | 1 | UniProt (O75554) Pfam (PF06220) Pfam (PF00397) In PDB | Homo sapiens (Human) | WBP-4,Formin-binding protein 21,WW domain-containing-binding protein 4 |
| 18 | R | Protein Red | polymer | 557 | 65731.5 | 1 | UniProt (Q13123) Pfam (PF07808) Pfam (PF07807) In PDB | Homo sapiens (Human) | Cytokine IK,IK factor,Protein RER |
| 19 | a, h, S | 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 |
| 20 | b, i, T | Small nuclear ribonucleoprotein F | polymer | 86 | 9734.2 | 3 | UniProt (P62306) Pfam (PF01423) In PDB | Homo sapiens (Human) | snRNP-F,Sm protein F,SmF |
| 21 | c, j, U | Small nuclear ribonucleoprotein E | polymer | 92 | 10817.6 | 3 | UniProt (P62304) Pfam (PF01423) In PDB | Homo sapiens (Human) | snRNP-E,Sm protein E,SmE |
| 22 | d, k, V | Small nuclear ribonucleoprotein G | polymer | 76 | 8508.1 | 3 | UniProt (P62308) Pfam (PF01423) In PDB | Homo sapiens (Human) | snRNP-G,Sm protein G,SmG |
| 23 | e, l, W | 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 |
| 24 | f, m, X | 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',SmB/B' |
| 25 | g, n, Z | 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 |
| 26 | o | U6 snRNA-associated Sm-like protein LSm2 | polymer | 95 | 10847.5 | 1 | UniProt (Q9Y333) Pfam (PF01423) In PDB | Homo sapiens (Human) | Protein G7b,Small nuclear ribonuclear protein D homolog,snRNP core Sm-like protein Sm-x5 |
| 27 | p | U6 snRNA-associated Sm-like protein LSm3 | polymer | 102 | 11859.4 | 1 | UniProt (P62310) Pfam (PF01423) In PDB | Homo sapiens (Human) | |
| 28 | q | U6 snRNA-associated Sm-like protein LSm4 | polymer | 139 | 15375.8 | 1 | UniProt (Q9Y4Z0) Pfam (PF01423) In PDB | Homo sapiens (Human) | Glycine-rich protein,GRP |
| 29 | r | U6 snRNA-associated Sm-like protein LSm5 | polymer | 91 | 9945.4 | 1 | UniProt (Q9Y4Y9) Pfam (PF01423) In PDB | Homo sapiens (Human) | |
| 30 | s | U6 snRNA-associated Sm-like protein LSm6 | polymer | 80 | 9139.6 | 1 | UniProt (P62312) Pfam (PF01423) In PDB | Homo sapiens (Human) | |
| 31 | t | U6 snRNA-associated Sm-like protein LSm7 | polymer | 103 | 11617.4 | 1 | UniProt (Q9UK45) Pfam (PF01423) In PDB | Homo sapiens (Human) | |
| 32 | u | U6 snRNA-associated Sm-like protein LSm8 | polymer | 96 | 10410.6 | 1 | UniProt (O95777) Pfam (PF01423) In PDB | Homo sapiens (Human) | |
| 33 | v | Splicing factor 3B subunit 1 | polymer | 1304 | 146024.9 | 1 | UniProt (O75533) Pfam (PF08920) Pfam (PF22646) In PDB | Homo sapiens (Human) | Pre-mRNA-splicing factor SF3b 155 kDa subunit,SF3b155,Spliceosome-associated protein 155,SAP 155 |
| 34 | w | Splicing factor 3B subunit 3 (SF3B3) | polymer | 1217 | 135718.8 | 1 | UniProt (Q15393) Pfam (PF10433) Pfam (PF03178) In PDB | Homo sapiens (Human) | |
| 35 | x | Splicing factor 3B subunit 5 | polymer | 86 | 10149.4 | 1 | UniProt (Q9BWJ5) Pfam (PF07189) In PDB | Homo sapiens (Human) | SF3b5,Pre-mRNA-splicing factor SF3b 10 kDa subunit |
| 36 | y | PHD finger-like domain-containing protein 5A | polymer | 110 | 12427.5 | 1 | UniProt (Q7RTV0) Pfam (PF03660) In PDB | Homo sapiens (Human) | PHD finger-like domain protein 5A,Splicing factor 3B-associated 14 kDa protein,SF3b14b |
| 37 | z | U2 small nuclear ribonucleoprotein A' | polymer | 256 | 28631.8 | 1 | UniProt (P09661) Pfam (PF14580) In PDB | Homo sapiens (Human) | U2 snRNP A' |
| 38 | 1 | U2 small nuclear ribonucleoprotein B'' | polymer | 225 | 25524.4 | 1 | UniProt (P08579) Pfam (PF00076) In PDB | Homo sapiens (Human) | U2 snRNP B'' |
| 39 | Y | MINX pre-mRNA | polymer | 324 | 103979.1 | 1 | Homo sapiens (Human) | ||
| 40 | 2 | Human gene for small nuclear RNA U2 (snRNA U2) | polymer | 188 | 60186.4 | 1 | GenBank (36516) | Homo sapiens (Human) | |
| 41 | 4 | Homo sapiens U4A snRNA | polymer | 145 | 46528.5 | 1 | GenBank (36174) | Homo sapiens (Human) | |
| 42 | 5 | Homo sapiens U5 A small nuclear RNA | polymer | 116 | 36908.7 | 1 | GenBank (36515) | Homo sapiens (Human) | |
| 43 | 6 | Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA | polymer | 106 | 34098.3 | 1 | REF (161087014) | Homo sapiens (Human) |
Sequence modifications
z: 1 - 255 (UniProt: P09661)
| PDB | External Database | Details |
|---|---|---|
| Asp 89 | Cys 89 | conflict |
| Cys 119 | Ser 119 | conflict |
| Phe 151 | - | insertion |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 57 |
| Total formula weight | 2389149.8 | |
| All* | Total formula weight | 2389149.8 |
