5MQF
Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | 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) | Homo sapiens (Human) | 220 kDa U5 snRNP-specific protein,PRP8 homolog,Splicing factor Prp8,p220 |
| 2 | B (B) | 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) | 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 (C) | SNW domain-containing protein 1 | polymer | 536 | 61610.7 | 1 | UniProt (Q13573) Pfam (PF02731) | Homo sapiens (Human) | Nuclear protein SkiP,Nuclear receptor coactivator NCoA-62,Ski-interacting protein |
| 4 | D (D) | Pleiotropic regulator 1 | polymer | 515 | 57379.8 | 1 | UniProt (O43660) Pfam (PF00400) | Homo sapiens (Human) | |
| 5 | E (E) | Pre-mRNA-processing factor 17 | polymer | 579 | 65612.2 | 1 | UniProt (O60508) Pfam (PF00400) | Homo sapiens (Human) | Cell division cycle 40 homolog,EH-binding protein 3,Ehb3,PRP17 homolog,hPRP17 |
| 6 | F (F) | U5 small nuclear ribonucleoprotein 40 kDa protein | polymer | 357 | 39359.5 | 1 | UniProt (Q96DI7) Pfam (PF00400) | Homo sapiens (Human) | U5-40K,38 kDa-splicing factor,Prp8-binding protein,hPRP8BP,U5 snRNP-specific 40 kDa protein,WD repeat-containing protein 57 |
| 7 | G, H, I, J (G, H, I, J) | Pre-mRNA-processing factor 19 | polymer | 504 | 55245.5 | 4 | UniProt (Q9UMS4) Pfam (PF04564) Pfam (PF08606) Pfam (PF00400) | Homo sapiens (Human) | Nuclear matrix protein 200,PRP19/PSO4 homolog,hPso4,Senescence evasion factor |
| 8 | K (K) | Pre-mRNA-splicing factor SPF27 | polymer | 225 | 26163.4 | 1 | UniProt (O75934) Pfam (PF05700) | Homo sapiens (Human) | Breast carcinoma-amplified sequence 2,DNA amplified in mammary carcinoma 1 protein,Spliceosome-associated protein SPF 27 |
| 9 | L (L) | Cell division cycle 5-like protein | polymer | 802 | 92406.9 | 1 | UniProt (Q99459) Pfam (PF13921) Pfam (PF11831) | Homo sapiens (Human) | Cdc5-like protein,Pombe cdc5-related protein |
| 10 | M (M) | Pre-mRNA-splicing factor SYF1 | polymer | 855 | 100148.7 | 1 | UniProt (Q9HCS7) Pfam (PF13181) | Homo sapiens (Human) | Protein HCNP,XPA-binding protein 2 |
| 11 | N (N) | Pre-mRNA-splicing factor SYF2 | polymer | 243 | 28780.5 | 1 | UniProt (O95926) Pfam (PF08231) | Homo sapiens (Human) | CCNDBP1-interactor,p29 |
| 12 | O (O) | Crooked neck-like protein 1 | polymer | 848 | 100610.0 | 1 | UniProt (Q9BZJ0) Pfam (PF02184) | Homo sapiens (Human) | Crooked neck homolog,hCrn |
| 13 | P (P) | Pre-mRNA-splicing factor RBM22 | polymer | 420 | 46959.6 | 1 | UniProt (Q9NW64) Pfam (PF21369) Pfam (PF00076) | Homo sapiens (Human) | RNA-binding motif protein 22,Zinc finger CCCH domain-containing protein 16 |
| 14 | Q (Q) | Protein BUD31 homolog | polymer | 144 | 17032.8 | 1 | UniProt (P41223) Pfam (PF01125) | Homo sapiens (Human) | Protein EDG-2,Protein G10 homolog |
| 15 | R (R) | Spliceosome-associated protein CWC15 homolog | polymer | 229 | 26674.4 | 1 | UniProt (Q9P013) Pfam (PF04889) | Homo sapiens (Human) | |
| 16 | S (S) | Serine/arginine repetitive matrix protein 2 | polymer | 2752 | 300255.3 | 1 | UniProt (Q9UQ35) Pfam (PF08312) | Homo sapiens (Human) | 300 kDa nuclear matrix antigen,Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa,Ser/Arg-related nuclear matrix protein of 300 kDa,Splicing coactivator subunit SRm300,Tax-responsive enhancer element-binding protein 803,TaxREB803 |
| 17 | T (T) | Pre-mRNA-splicing factor CWC22 homolog | polymer | 908 | 105646.6 | 1 | UniProt (Q9HCG8) Pfam (PF02854) Pfam (PF02847) | Homo sapiens (Human) | Nucampholin homolog,fSAPb |
| 18 | U (U) | Intron-binding protein aquarius | polymer | 1485 | 173003.1 | 1 | UniProt (O60306) Pfam (PF16399) Pfam (PF21143) Pfam (PF21144) Pfam (PF13086) Pfam (PF13087) | Homo sapiens (Human) | Intron-binding protein of 160 kDa,IBP160 |
| 19 | V (V) | Peptidyl-prolyl cis-trans isomerase-like 1 | polymer | 166 | 18257.8 | 1 | UniProt (Q9Y3C6) Pfam (PF00160) | Homo sapiens (Human) | PPIase,Rotamase PPIL1 |
| 20 | W (W) | U2 small nuclear ribonucleoprotein A' | polymer | 255 | 28484.6 | 1 | UniProt (P09661) Pfam (PF14580) | Homo sapiens (Human) | U2 snRNP A' |
| 21 | X (X) | U2 small nuclear ribonucleoprotein B'' | polymer | 225 | 25524.4 | 1 | UniProt (P08579) Pfam (PF00076) | Homo sapiens (Human) | U2 snRNP B'' |
| 22 | FA, Y (a, h) | Small nuclear ribonucleoprotein Sm D2 | polymer | 118 | 13551.9 | 2 | UniProt (P62316) Pfam (PF01423) | Homo sapiens (Human) | Sm-D2,snRNP core protein D2 |
| 23 | GA, Z (b, i) | Small nuclear ribonucleoprotein F | polymer | 86 | 9734.2 | 2 | UniProt (P62306) Pfam (PF01423) | Homo sapiens (Human) | snRNP-F,Sm protein F,SmF |
| 24 | AA, HA (c, j) | Small nuclear ribonucleoprotein E | polymer | 92 | 10817.6 | 2 | UniProt (P62304) Pfam (PF01423) | Homo sapiens (Human) | snRNP-E,Sm protein E,SmE |
| 25 | BA, IA (d, k) | Small nuclear ribonucleoprotein G | polymer | 76 | 8508.1 | 2 | UniProt (P62308) Pfam (PF01423) | Homo sapiens (Human) | snRNP-G,Sm protein G,SmG |
| 26 | CA, JA (e, l) | Small nuclear ribonucleoprotein Sm D3 | polymer | 126 | 13940.3 | 2 | UniProt (P62318) Pfam (PF01423) | Homo sapiens (Human) | Sm-D3,snRNP core protein D3 |
| 27 | DA, KA (f, m) | Small nuclear ribonucleoprotein-associated proteins B and B' | polymer | 240 | 24642.1 | 2 | UniProt (P14678) Pfam (PF01423) | Homo sapiens (Human) | snRNP-B,Sm protein B/B',SmB/B' |
| 28 | EA, LA (g, n) | Small nuclear ribonucleoprotein Sm D1 | polymer | 119 | 13310.7 | 2 | UniProt (P62314) Pfam (PF01423) | Homo sapiens (Human) | Sm-D1,Sm-D autoantigen,snRNP core protein D1 |
| 29 | MA (o) | Peptidyl-prolyl cis-trans isomerase E | polymer | 301 | 33475.8 | 1 | UniProt (Q9UNP9) Pfam (PF00076) Pfam (PF00160) | Homo sapiens (Human) | PPIase E,Cyclophilin E,Cyclophilin-33,Rotamase E |
| 30 | NA (p) | Eukaryotic initiation factor 4A-III | polymer | 411 | 46931.0 | 1 | UniProt (P38919) Pfam (PF00270) Pfam (PF00271) | Homo sapiens (Human) | eIF4A-III,ATP-dependent RNA helicase DDX48,ATP-dependent RNA helicase eIF4A-3,DEAD box protein 48,Eukaryotic initiation factor 4A-like NUK-34,Eukaryotic translation initiation factor 4A isoform 3,Nuclear matrix protein 265,hNMP 265 |
| 31 | OA (q) | ATP-dependent RNA helicase DHX8 | polymer | 1218 | 139252.0 | 1 | UniProt (Q14562) Pfam (PF00575) Pfam (PF00270) Pfam (PF00271) Pfam (PF04408) Pfam (PF21010) Pfam (PF07717) | Homo sapiens (Human) | DEAH box protein 8,RNA helicase HRH1 |
| 32 | PA, QA (Y, Z) | MINX pre-mRNA (intron) | polymer | 324 | 104019.2 | 2 | Homo sapiens (Human) | ||
| 33 | RA (2) | Human gene for small nuclear RNA U2 (snRNA U2) | polymer | 188 | 60186.4 | 1 | GenBank (36516) | Homo sapiens (Human) | |
| 34 | SA (5) | Homo sapiens U5 A small nuclear RNA | polymer | 116 | 36908.7 | 1 | GenBank (36515) | Homo sapiens (Human) | |
| 35 | TA (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
D: 1 - 515 (UniProt: O43660)
W: 1 - 255 (UniProt: P09661)
q: 3 - 1215 (UniProt: Q14562)
| PDB | External Database | Details |
|---|---|---|
| Ala 454 | Val 454 | conflict |
| Val 455 | Gln 455 | conflict |
| Gln 456 | Pro 456 | conflict |
| Pro 457 | Gly 457 | conflict |
| Gly 458 | Ser 458 | conflict |
| Ser 459 | Leu 459 | conflict |
| Leu 460 | Asp 460 | conflict |
| Asp 461 | Ser 461 | conflict |
| Asp 492 | - | insertion |
| PDB | External Database | Details |
|---|---|---|
| Asp 89 | Cys 89 | conflict |
| Cys 119 | Ser 119 | conflict |
| PDB | External Database | Details |
|---|---|---|
| - | Met 946 | deletion |
| - | Asp 947 | deletion |
| Gly 948 | Ala 948 | conflict |
| Ser 949 | Pro 949 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 46 |
| Total formula weight | 2666327.6 | |
| All* | Total formula weight | 2666327.6 |
