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 | 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) In PDB | Homo sapiens (Human) | 220 kDa U5 snRNP-specific protein,PRP8 homolog,Splicing factor Prp8,p220 |
| 2 | B | U5 snRNA | polymer | 117 | 37254.9 | 1 | Homo sapiens | ||
| 3 | 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) 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 |
| 4 | D | 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 |
| 5 | E | 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 |
| 6 | F | U6 snRNA | polymer | 107 | 34404.4 | 1 | Homo sapiens | ||
| 7 | G | Pre-mRNA | polymer | 275 | 88088.8 | 1 | Homo sapiens (Human) | ||
| 8 | H | U2 snRNA | polymer | 188 | 60186.4 | 1 | Homo sapiens | ||
| 9 | I | Pre-mRNA-splicing factor SYF1 | polymer | 855 | 100148.7 | 1 | UniProt (Q9HCS7) Pfam (PF13181) In PDB | Homo sapiens (Human) | Protein HCNP,XPA-binding protein 2 |
| 10 | J | Crooked neck-like protein 1 | polymer | 848 | 100610.0 | 1 | UniProt (Q9BZJ0) Pfam (PF02184) In PDB | Homo sapiens (Human) | Crooked neck homolog,hCrn |
| 11 | K | Pre-mRNA-splicing factor SPF27 | polymer | 225 | 26163.4 | 1 | UniProt (O75934) Pfam (PF05700) In PDB | Homo sapiens (Human) | Breast carcinoma-amplified sequence 2,DNA amplified in mammary carcinoma 1 protein,Spliceosome-associated protein SPF 27 |
| 12 | L | Cell division cycle 5-like protein | polymer | 802 | 92406.9 | 1 | UniProt (Q99459) Pfam (PF13921) Pfam (PF11831) In PDB | Homo sapiens (Human) | Cdc5-like protein,Pombe cdc5-related protein |
| 13 | y | Pre-mRNA-splicing factor ISY1 homolog | polymer | 307 | 35499.1 | 1 | UniProt (Q9ULR0) Pfam (PF06246) In PDB | Homo sapiens (Human) | |
| 14 | M | Pre-mRNA-splicing factor SYF2 | polymer | 243 | 28780.5 | 1 | UniProt (O95926) Pfam (PF08231) In PDB | Homo sapiens (Human) | CCNDBP1-interactor,p29 |
| 15 | N | Protein BUD31 homolog | polymer | 144 | 17032.8 | 1 | UniProt (P41223) Pfam (PF01125) In PDB | Homo sapiens (Human) | Protein EDG-2,Protein G10 homolog |
| 16 | O | Pre-mRNA-splicing factor RBM22 | polymer | 420 | 46959.6 | 1 | UniProt (Q9NW64) Pfam (PF21369) Pfam (PF00076) In PDB | Homo sapiens (Human) | RNA-binding motif protein 22,Zinc finger CCCH domain-containing protein 16 |
| 17 | P | Spliceosome-associated protein CWC15 homolog | polymer | 229 | 26674.4 | 1 | UniProt (Q9P013) Pfam (PF04889) In PDB | Homo sapiens (Human) | |
| 18 | R | SNW domain-containing protein 1 | polymer | 536 | 61770.6 | 1 | UniProt (Q13573) Pfam (PF02731) In PDB | Homo sapiens (Human) | Nuclear protein SkiP,Nuclear receptor coactivator NCoA-62,Ski-interacting protein |
| 19 | S | Peptidyl-prolyl cis-trans isomerase-like 1 | polymer | 166 | 18257.8 | 1 | UniProt (Q9Y3C6) Pfam (PF00160) In PDB | Homo sapiens (Human) | PPIase,Rotamase PPIL1 |
| 20 | T | Pleiotropic regulator 1 | polymer | 514 | 57280.8 | 1 | UniProt (O43660) Pfam (PF00400) In PDB | Homo sapiens (Human) | |
| 21 | Q | Intron-binding protein aquarius | polymer | 1485 | 171502.5 | 1 | UniProt (O60306) Pfam (PF16399) Pfam (PF21143) Pfam (PF21144) Pfam (PF13086) Pfam (PF13087) In PDB | Homo sapiens (Human) | Intron-binding protein of 160 kDa,IBP160 |
| 22 | U | Serine/arginine repetitive matrix protein 2 | polymer | 2752 | 300255.3 | 1 | UniProt (Q9UQ35) Pfam (PF08312) In PDB | 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 | V | Pre-mRNA-splicing factor CWC22 homolog | polymer | 908 | 105646.6 | 1 | UniProt (Q9HCG8) Pfam (PF02854) Pfam (PF02847) In PDB | Homo sapiens (Human) | Nucampholin homolog,fSAPb |
| 24 | W | Pre-mRNA-processing factor 17 | polymer | 579 | 65612.2 | 1 | UniProt (O60508) Pfam (PF00400) In PDB | Homo sapiens (Human) | Cell division cycle 40 homolog,EH-binding protein 3,Ehb3,PRP17 homolog,hPRP17 |
| 25 | X | Pre-mRNA-splicing factor CWC25 homolog | polymer | 425 | 49736.8 | 1 | UniProt (Q9NXE8) Pfam (PF10197) Pfam (PF12542) In PDB | Homo sapiens (Human) | Coiled-coil domain-containing protein 49,Spliceosome-associated protein homolog CWC25 |
| 26 | Y | Coiled-coil domain-containing protein 94 | polymer | 323 | 37141.8 | 1 | UniProt (Q9BW85) Pfam (PF04502) In PDB | Homo sapiens (Human) | |
| 27 | 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) In PDB | Homo sapiens (Human) | ATP-dependent RNA helicase DHX38,DEAH box protein 38 |
| 28 | q, r, s, t | Pre-mRNA-processing factor 19 | polymer | 504 | 55245.5 | 4 | UniProt (Q9UMS4) Pfam (PF04564) Pfam (PF08606) Pfam (PF00400) In PDB | Homo sapiens (Human) | Nuclear matrix protein 200,PRP19/PSO4 homolog,hPso4,RING-type E3 ubiquitin transferase PRP19,Senescence evasion factor |
| 29 | u | Eukaryotic initiation factor 4A-III | polymer | 411 | 46931.0 | 1 | UniProt (P38919) Pfam (PF00270) Pfam (PF00271) In PDB | 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 | v | Protein mago nashi homolog 2 | polymer | 148 | 17301.8 | 1 | UniProt (Q96A72) Pfam (PF02792) In PDB | Homo sapiens (Human) | |
| 31 | w | RNA-binding protein 8A | polymer | 174 | 19925.1 | 1 | UniProt (Q9Y5S9) Pfam (PF00076) In PDB | Homo sapiens (Human) | Binder of OVCA1-1,BOV-1,RNA-binding motif protein 8A,RNA-binding protein Y14,Ribonucleoprotein RBM8A |
| 32 | x | Protein CASC3 | polymer | 703 | 76382.0 | 1 | UniProt (O15234) Pfam (PF09405) In PDB | Homo sapiens (Human) | Cancer susceptibility candidate gene 3 protein,Metastatic lymph node gene 51 protein,MLN 51,Protein barentsz,Btz |
| 33 | h, a | Small nuclear ribonucleoprotein Sm D3 | polymer | 126 | 13940.3 | 2 | UniProt (P62318) Pfam (PF01423) In PDB | Homo sapiens (Human) | Sm-D3,snRNP core protein D3 |
| 34 | i, b | Small nuclear ribonucleoprotein-associated proteins B and B' | polymer | 229 | 23459.7 | 2 | UniProt (P14678) Pfam (PF01423) In PDB | Homo sapiens (Human) | snRNP-B,Sm protein B/B',SmB/B' |
| 35 | j, c | Small nuclear ribonucleoprotein Sm D1 | polymer | 119 | 13310.7 | 2 | UniProt (P62314) Pfam (PF01423) In PDB | Homo sapiens (Human) | Sm-D1,Sm-D autoantigen,snRNP core protein D1 |
| 36 | k, d | Small nuclear ribonucleoprotein Sm D2 | polymer | 118 | 13551.9 | 2 | UniProt (P62316) Pfam (PF01423) In PDB | Homo sapiens (Human) | Sm-D2,snRNP core protein D2 |
| 37 | m, f | Small nuclear ribonucleoprotein F | polymer | 86 | 9734.2 | 2 | UniProt (P62306) Pfam (PF01423) In PDB | Homo sapiens (Human) | snRNP-F,Sm protein F,SmF |
| 38 | l, e | Small nuclear ribonucleoprotein E | polymer | 92 | 10817.6 | 2 | UniProt (P62304) Pfam (PF01423) In PDB | Homo sapiens (Human) | snRNP-E,Sm protein E,SmE |
| 39 | n, g | Small nuclear ribonucleoprotein G | polymer | 76 | 8508.1 | 2 | UniProt (P62308) Pfam (PF01423) In PDB | Homo sapiens (Human) | snRNP-G,Sm protein G,SmG |
| 40 | o | U2 small nuclear ribonucleoprotein A' | polymer | 255 | 28456.6 | 1 | UniProt (P09661) Pfam (PF14580) In PDB | Homo sapiens (Human) | U2 snRNP A' |
| 41 | p | U2 small nuclear ribonucleoprotein B'' | polymer | 225 | 25524.4 | 1 | UniProt (P08579) Pfam (PF00076) In PDB | Homo sapiens (Human) | U2 snRNP B'' |
| 42 | 1 | Peptidyl-prolyl cis-trans isomerase E | polymer | 301 | 33475.8 | 1 | UniProt (Q9UNP9) Pfam (PF00076) Pfam (PF00160) In PDB | Homo sapiens (Human) | PPIase E,Cyclophilin E,Cyclophilin-33,Rotamase E |
| 43 | 2 | Peptidylprolyl isomerase domain and WD repeat-containing protein 1 | polymer | 646 | 73679.9 | 1 | UniProt (Q96BP3) Pfam (PF00400) Pfam (PF00160) In PDB | Homo sapiens (Human) | Spliceosome-associated cyclophilin |
| 44 | 3 | Peptidyl-prolyl cis-trans isomerase G | polymer | 754 | 88854.3 | 1 | UniProt (Q13427) Pfam (PF00160) In PDB | Homo sapiens (Human) | Peptidyl-prolyl isomerase G,CASP10,Clk-associating RS-cyclophilin,SRcyp,Cyclophilin G,Rotamase G |
| 45 | 4 | UNKNOW | polymer | 37 | 2631.9 | 1 | Homo sapiens | ||
| 46 | A | INOSITOL HEXAKISPHOSPHATE | non-polymer | 660.0 | 1 | Chemie (IHP) | |||
| 47 | C | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 1 | Chemie (GTP) | |||
| 48 | C, F, u | MAGNESIUM ION | non-polymer | 24.3 | 7 | Chemie (MG) | |||
| 49 | D | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 2 | Chemie (ADP) | |||
| 50 | N, O, Y | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) | |||
| 51 | 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 |
