5YZG
The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution
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 (A) | Pre-mRNA-processing-splicing factor 8 | polymer | 2335 | 273974.3 | 1 | UniProt (Q6P2Q9) Pfam (PF10598) Pfam (PF10597) Pfam (PF10596) Pfam (PF12134) Pfam (PF01398) Pfam (PF08084) Pfam (PF08082) Pfam (PF08083) | Homo sapiens (Human) | 220 kDa U5 snRNP-specific protein,PRP8 homolog,Splicing factor Prp8,p220 |
| 2 | B (B) | U5 snRNA | polymer | 117 | 37254.9 | 1 | Homo sapiens | ||
| 3 | C (C) | 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) | Homo sapiens (Human) | Elongation factor Tu GTP-binding domain-containing protein 2,SNU114 homolog,hSNU114,U5 snRNP-specific protein,116 kDa,U5-116 kDa |
| 4 | D (D) | U5 small nuclear ribonucleoprotein 200 kDa helicase | polymer | 2136 | 244823.4 | 1 | UniProt (O75643) Pfam (PF21188) Pfam (PF18149) Pfam (PF00270) Pfam (PF00271) Pfam (PF23445) Pfam (PF02889) | Homo sapiens (Human) | Activating signal cointegrator 1 complex subunit 3-like 1,BRR2 homolog,U5 snRNP-specific 200 kDa protein,U5-200KD |
| 5 | E (E) | 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 |
| 6 | F (F) | U6 snRNA | polymer | 107 | 34404.4 | 1 | Homo sapiens | ||
| 7 | G (G) | Pre-mRNA | polymer | 275 | 88088.8 | 1 | Homo sapiens (Human) | ||
| 8 | H (H) | U2 snRNA | polymer | 188 | 60186.4 | 1 | Homo sapiens | ||
| 9 | I (I) | Pre-mRNA-splicing factor SYF1 | polymer | 855 | 100148.7 | 1 | UniProt (Q9HCS7) Pfam (PF23233) Pfam (PF23220) Pfam (PF23231) | Homo sapiens (Human) | Protein HCNP,XPA-binding protein 2 |
| 10 | J (J) | Crooked neck-like protein 1 | polymer | 848 | 100610.0 | 1 | UniProt (Q9BZJ0) Pfam (PF23231) | Homo sapiens (Human) | Crooked neck homolog,hCrn |
| 11 | 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 |
| 12 | 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 |
| 13 | M (y) | Pre-mRNA-splicing factor ISY1 homolog | polymer | 307 | 35499.1 | 1 | UniProt (Q9ULR0) Pfam (PF06246) | Homo sapiens (Human) | |
| 14 | N (M) | Pre-mRNA-splicing factor SYF2 | polymer | 243 | 28780.5 | 1 | UniProt (O95926) Pfam (PF08231) | Homo sapiens (Human) | CCNDBP1-interactor,p29 |
| 15 | O (N) | Protein BUD31 homolog | polymer | 144 | 17032.8 | 1 | UniProt (P41223) Pfam (PF01125) | Homo sapiens (Human) | Protein EDG-2,Protein G10 homolog |
| 16 | P (O) | Pre-mRNA-splicing factor RBM22 | polymer | 420 | 46959.6 | 1 | UniProt (Q9NW64) Pfam (PF21369) Pfam (PF25584) Pfam (PF00076) | Homo sapiens (Human) | RNA-binding motif protein 22,Zinc finger CCCH domain-containing protein 16 |
| 17 | Q (P) | Spliceosome-associated protein CWC15 homolog | polymer | 229 | 26674.4 | 1 | UniProt (Q9P013) Pfam (PF04889) | Homo sapiens (Human) | |
| 18 | R (R) | SNW domain-containing protein 1 | polymer | 536 | 61770.6 | 1 | UniProt (Q13573) Pfam (PF02731) | Homo sapiens (Human) | Nuclear protein SkiP,Nuclear receptor coactivator NCoA-62,Ski-interacting protein |
| 19 | S (S) | Peptidyl-prolyl cis-trans isomerase-like 1 | polymer | 166 | 18257.8 | 1 | UniProt (Q9Y3C6) Pfam (PF00160) | Homo sapiens (Human) | PPIase,Rotamase PPIL1 |
| 20 | T (T) | Pleiotropic regulator 1 | polymer | 514 | 57280.8 | 1 | UniProt (O43660) Pfam (PF00400) | Homo sapiens (Human) | |
| 21 | U (Q) | Intron-binding protein aquarius | polymer | 1485 | 171502.5 | 1 | UniProt (O60306) Pfam (PF16399) Pfam (PF21143) Pfam (PF21144) Pfam (PF13086) Pfam (PF13087) | Homo sapiens (Human) | Intron-binding protein of 160 kDa,IBP160 |
| 22 | V (U) | 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 |
| 23 | W (V) | Pre-mRNA-splicing factor CWC22 homolog | polymer | 908 | 105646.6 | 1 | UniProt (Q9HCG8) Pfam (PF02854) Pfam (PF02847) | Homo sapiens (Human) | Nucampholin homolog,fSAPb |
| 24 | X (W) | 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 |
| 25 | Y (X) | Pre-mRNA-splicing factor CWC25 homolog | polymer | 425 | 49736.8 | 1 | UniProt (Q9NXE8) Pfam (PF10197) Pfam (PF12542) | Homo sapiens (Human) | Coiled-coil domain-containing protein 49,Spliceosome-associated protein homolog CWC25 |
| 26 | Z (Y) | Coiled-coil domain-containing protein 94 | polymer | 323 | 37141.8 | 1 | UniProt (Q9BW85) Pfam (PF04502) | Homo sapiens (Human) | |
| 27 | AA (Z) | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 | polymer | 1227 | 140720.6 | 1 | UniProt (Q92620) Pfam (PF00270) Pfam (PF00271) Pfam (PF04408) Pfam (PF21010) Pfam (PF07717) | Homo sapiens (Human) | ATP-dependent RNA helicase DHX38,DEAH box protein 38 |
| 28 | BA, CA, DA, EA (q, r, s, t) | Pre-mRNA-processing factor 19 | polymer | 504 | 55245.5 | 4 | UniProt (Q9UMS4) Pfam (PF04564) Pfam (PF08606) Pfam (PF24814) | Homo sapiens (Human) | Nuclear matrix protein 200,PRP19/PSO4 homolog,hPso4,RING-type E3 ubiquitin transferase PRP19,Senescence evasion factor |
| 29 | FA (u) | 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 |
| 30 | GA (v) | Protein mago nashi homolog 2 | polymer | 148 | 17301.8 | 1 | UniProt (Q96A72) Pfam (PF02792) | Homo sapiens (Human) | |
| 31 | HA (w) | RNA-binding protein 8A | polymer | 174 | 19925.1 | 1 | UniProt (Q9Y5S9) Pfam (PF00076) | Homo sapiens (Human) | Binder of OVCA1-1,BOV-1,RNA-binding motif protein 8A,RNA-binding protein Y14,Ribonucleoprotein RBM8A |
| 32 | IA (x) | Protein CASC3 | polymer | 703 | 76382.0 | 1 | UniProt (O15234) Pfam (PF09405) | Homo sapiens (Human) | Cancer susceptibility candidate gene 3 protein,Metastatic lymph node gene 51 protein,MLN 51,Protein barentsz,Btz |
| 33 | JA, SA (h, a) | Small nuclear ribonucleoprotein Sm D3 | polymer | 126 | 13940.3 | 2 | UniProt (P62318) Pfam (PF01423) | Homo sapiens (Human) | Sm-D3,snRNP core protein D3 |
| 34 | KA, TA (i, b) | Small nuclear ribonucleoprotein-associated proteins B and B' | polymer | 229 | 23459.7 | 2 | UniProt (P14678) Pfam (PF01423) | Homo sapiens (Human) | snRNP-B,Sm protein B/B',SmB/B' |
| 35 | LA, UA (j, c) | 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 |
| 36 | MA, VA (k, d) | Small nuclear ribonucleoprotein Sm D2 | polymer | 118 | 13551.9 | 2 | UniProt (P62316) Pfam (PF01423) | Homo sapiens (Human) | Sm-D2,snRNP core protein D2 |
| 37 | NA, WA (m, f) | Small nuclear ribonucleoprotein F | polymer | 86 | 9734.2 | 2 | UniProt (P62306) Pfam (PF01423) | Homo sapiens (Human) | snRNP-F,Sm protein F,SmF |
| 38 | OA, XA (l, e) | Small nuclear ribonucleoprotein E | polymer | 92 | 10817.6 | 2 | UniProt (P62304) Pfam (PF01423) | Homo sapiens (Human) | snRNP-E,Sm protein E,SmE |
| 39 | PA, YA (n, g) | Small nuclear ribonucleoprotein G | polymer | 76 | 8508.1 | 2 | UniProt (P62308) Pfam (PF01423) | Homo sapiens (Human) | snRNP-G,Sm protein G,SmG |
| 40 | QA (o) | U2 small nuclear ribonucleoprotein A' | polymer | 255 | 28456.6 | 1 | UniProt (P09661) Pfam (PF14580) | Homo sapiens (Human) | U2 snRNP A' |
| 41 | RA (p) | U2 small nuclear ribonucleoprotein B'' | polymer | 225 | 25524.4 | 1 | UniProt (P08579) Pfam (PF00076) | Homo sapiens (Human) | U2 snRNP B'' |
| 42 | ZA (1) | 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 |
| 43 | AB (2) | Peptidylprolyl isomerase domain and WD repeat-containing protein 1 | polymer | 646 | 73679.9 | 1 | UniProt (Q96BP3) Pfam (PF00400) Pfam (PF00160) | Homo sapiens (Human) | Spliceosome-associated cyclophilin |
| 44 | BB (3) | Peptidyl-prolyl cis-trans isomerase G | polymer | 754 | 88854.3 | 1 | UniProt (Q13427) Pfam (PF00160) | Homo sapiens (Human) | Peptidyl-prolyl isomerase G,CASP10,Clk-associating RS-cyclophilin,SRcyp,Cyclophilin G,Rotamase G |
| 45 | CB (4) | UNKNOW | polymer | 37 | 2631.9 | 1 | Homo sapiens | ||
| 46 | DB (A) | INOSITOL HEXAKISPHOSPHATE | non-polymer | 660.0 | 1 | Chemie (IHP) | |||
| 47 | EB (C) | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 1 | Chemie (GTP) PubChem (177679032) PubChem (135400627) PubChem (135487750) PubChem (136088935) PubChem (136803486) PubChem (135398633) PubChem (135544356) PubChem (135547949) PubChem (135600366) PubChem (135749822) PubChem (136005188) PubChem (136073923) PubChem (136240914) PubChem (136664747) PubChem (136772743) PubChem (136772744) PubChem (136803487) PubChem (137286749) PubChem (164715984) PubChem (171699466) | |||
| 48 | FB, IB, JB, KB, LB... (C, F, u) | MAGNESIUM ION | non-polymer | 24.3 | 7 | Chemie (MG) PubChem (888) | |||
| 49 | GB, HB (D) | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 2 | Chemie (ADP) | |||
| 50 | NB, OB, PB, QB, RB... (N, O, Y) | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) | |||
| 51 | VB (u) | ADENOSINE-5'-TRIPHOSPHATE | non-polymer | 507.2 | 1 | Chemie (ATP) |
Sequence modifications
X: 1 - 425 (UniProt: Q9NXE8)
| PDB | External Database | Details |
|---|---|---|
| Gln 145 | Lys 145 | conflict |
| Pro 149 | Lys 149 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 55 |
| Total formula weight | 3190642.5 | |
| Non-Polymers* | Number of molecules | 19 |
| Total formula weight | 3172.8 | |
| All* | Total formula weight | 3193815.3 |
