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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5MQF

Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1APre-mRNA-processing-splicing factor 8polymer2335273974.31UniProt (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
2B116 kDa U5 small nuclear ribonucleoprotein componentpolymer972109560.61UniProt (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
3CSNW domain-containing protein 1polymer53661610.71UniProt (Q13573)
Pfam (PF02731)
In PDB		Homo sapiens (Human)Nuclear protein SkiP,Nuclear receptor coactivator NCoA-62,Ski-interacting protein
4DPleiotropic regulator 1polymer51557379.81UniProt (O43660)
Pfam (PF00400)
In PDB		Homo sapiens (Human)
5EPre-mRNA-processing factor 17polymer57965612.21UniProt (O60508)
Pfam (PF00400)
In PDB		Homo sapiens (Human)Cell division cycle 40 homolog,EH-binding protein 3,Ehb3,PRP17 homolog,hPRP17
6FU5 small nuclear ribonucleoprotein 40 kDa proteinpolymer35739359.51UniProt (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
7G, H, I, JPre-mRNA-processing factor 19polymer50455245.54UniProt (Q9UMS4)
Pfam (PF04564)
Pfam (PF08606)
Pfam (PF00400)
In PDB		Homo sapiens (Human)Nuclear matrix protein 200,PRP19/PSO4 homolog,hPso4,Senescence evasion factor
8KPre-mRNA-splicing factor SPF27polymer22526163.41UniProt (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
9LCell division cycle 5-like proteinpolymer80292406.91UniProt (Q99459)
Pfam (PF13921)
Pfam (PF11831)
In PDB		Homo sapiens (Human)Cdc5-like protein,Pombe cdc5-related protein
10MPre-mRNA-splicing factor SYF1polymer855100148.71UniProt (Q9HCS7)
Pfam (PF13181)
In PDB		Homo sapiens (Human)Protein HCNP,XPA-binding protein 2
11NPre-mRNA-splicing factor SYF2polymer24328780.51UniProt (O95926)
Pfam (PF08231)
In PDB		Homo sapiens (Human)CCNDBP1-interactor,p29
12OCrooked neck-like protein 1polymer848100610.01UniProt (Q9BZJ0)
Pfam (PF02184)
In PDB		Homo sapiens (Human)Crooked neck homolog,hCrn
13PPre-mRNA-splicing factor RBM22polymer42046959.61UniProt (Q9NW64)
Pfam (PF21369)
Pfam (PF00076)
In PDB		Homo sapiens (Human)RNA-binding motif protein 22,Zinc finger CCCH domain-containing protein 16
14QProtein BUD31 homologpolymer14417032.81UniProt (P41223)
Pfam (PF01125)
In PDB		Homo sapiens (Human)Protein EDG-2,Protein G10 homolog
15RSpliceosome-associated protein CWC15 homologpolymer22926674.41UniProt (Q9P013)
Pfam (PF04889)
In PDB		Homo sapiens (Human)
16SSerine/arginine repetitive matrix protein 2polymer2752300255.31UniProt (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
17TPre-mRNA-splicing factor CWC22 homologpolymer908105646.61UniProt (Q9HCG8)
Pfam (PF02854)
Pfam (PF02847)
In PDB		Homo sapiens (Human)Nucampholin homolog,fSAPb
18UIntron-binding protein aquariuspolymer1485173003.11UniProt (O60306)
Pfam (PF16399)
Pfam (PF21143)
Pfam (PF21144)
Pfam (PF13086)
Pfam (PF13087)
In PDB		Homo sapiens (Human)Intron-binding protein of 160 kDa,IBP160
19VPeptidyl-prolyl cis-trans isomerase-like 1polymer16618257.81UniProt (Q9Y3C6)
Pfam (PF00160)
In PDB		Homo sapiens (Human)PPIase,Rotamase PPIL1
20WU2 small nuclear ribonucleoprotein A'polymer25528484.61UniProt (P09661)
Pfam (PF14580)
In PDB		Homo sapiens (Human)U2 snRNP A'
21XU2 small nuclear ribonucleoprotein B''polymer22525524.41UniProt (P08579)
Pfam (PF00076)
In PDB		Homo sapiens (Human)U2 snRNP B''
22a, hSmall nuclear ribonucleoprotein Sm D2polymer11813551.92UniProt (P62316)
Pfam (PF01423)
In PDB		Homo sapiens (Human)Sm-D2,snRNP core protein D2
23b, iSmall nuclear ribonucleoprotein Fpolymer869734.22UniProt (P62306)
Pfam (PF01423)
In PDB		Homo sapiens (Human)snRNP-F,Sm protein F,SmF
24c, jSmall nuclear ribonucleoprotein Epolymer9210817.62UniProt (P62304)
Pfam (PF01423)
In PDB		Homo sapiens (Human)snRNP-E,Sm protein E,SmE
25d, kSmall nuclear ribonucleoprotein Gpolymer768508.12UniProt (P62308)
Pfam (PF01423)
In PDB		Homo sapiens (Human)snRNP-G,Sm protein G,SmG
26e, lSmall nuclear ribonucleoprotein Sm D3polymer12613940.32UniProt (P62318)
Pfam (PF01423)
In PDB		Homo sapiens (Human)Sm-D3,snRNP core protein D3
27f, mSmall nuclear ribonucleoprotein-associated proteins B and B'polymer24024642.12UniProt (P14678)
Pfam (PF01423)
In PDB		Homo sapiens (Human)snRNP-B,Sm protein B/B',SmB/B'
28g, nSmall nuclear ribonucleoprotein Sm D1polymer11913310.72UniProt (P62314)
Pfam (PF01423)
In PDB		Homo sapiens (Human)Sm-D1,Sm-D autoantigen,snRNP core protein D1
29oPeptidyl-prolyl cis-trans isomerase Epolymer30133475.81UniProt (Q9UNP9)
Pfam (PF00076)
Pfam (PF00160)
In PDB		Homo sapiens (Human)PPIase E,Cyclophilin E,Cyclophilin-33,Rotamase E
30pEukaryotic initiation factor 4A-IIIpolymer41146931.01UniProt (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
31qATP-dependent RNA helicase DHX8polymer1218139252.01UniProt (Q14562)
Pfam (PF00575)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF04408)
Pfam (PF21010)
Pfam (PF07717)
In PDB		Homo sapiens (Human)DEAH box protein 8,RNA helicase HRH1
32Y, ZMINX pre-mRNA (intron)polymer324104019.22Homo sapiens (Human)
332Human gene for small nuclear RNA U2 (snRNA U2)polymer18860186.41GenBank (36516)Homo sapiens (Human)
345Homo sapiens U5 A small nuclear RNApolymer11636908.71GenBank (36515)Homo sapiens (Human)
356Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNApolymer10634098.31REF (161087014)Homo sapiens (Human)
Sequence modifications
D: 1 - 515 (UniProt: O43660)
PDBExternal DatabaseDetails
Ala 454Val 454conflict
Val 455Gln 455conflict
Gln 456Pro 456conflict
Pro 457Gly 457conflict
Gly 458Ser 458conflict
Ser 459Leu 459conflict
Leu 460Asp 460conflict
Asp 461Ser 461conflict
Asp 492-insertion
W: 1 - 255 (UniProt: P09661)
PDBExternal DatabaseDetails
Asp 89Cys 89conflict
Cys 119Ser 119conflict
q: 3 - 1215 (UniProt: Q14562)
PDBExternal DatabaseDetails
-Met 946deletion
-Asp 947deletion
Gly 948Ala 948conflict
Ser 949Pro 949conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains46
Total formula weight2666327.6
All*Total formula weight2666327.6
*Water molecules are not included.

220113

PDB entries from 2024-05-22

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