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5XJC

Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(A)
Pre-mRNA-processing-splicing factor 8polymer2335273974.31UniProt (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
2B
(B)
U5 snRNApolymer11737254.91Homo sapiens
3C
(C)
116 kDa U5 small nuclear ribonucleoprotein componentpolymer972109560.61UniProt (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
4D
(D)
U5 small nuclear ribonucleoprotein 200 kDa helicasepolymer2136244823.41UniProt (O75643)
Pfam (PF21188)
Pfam (PF18149)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF02889)
Homo sapiens (Human)Activating signal cointegrator 1 complex subunit 3-like 1,BRR2 homolog,U5 snRNP-specific 200 kDa protein,U5-200KD
5E
(E)
U5 small nuclear ribonucleoprotein 40 kDa proteinpolymer35739359.51UniProt (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
6F
(F)
U6 snRNApolymer10734404.41Homo sapiens
7G
(G)
pre-mRNApolymer27587977.81Human adenovirus 2
8H
(H)
Homo sapiens small nuclear RNA (U2) genepolymer18860186.41GenBank (609501)Homo sapiens
9I
(I)
Pre-mRNA-splicing factor SYF1polymer855100148.71UniProt (Q9HCS7)
Pfam (PF13181)
Homo sapiens (Human)Protein HCNP,XPA-binding protein 2
10J
(J)
Crooked neck-like protein 1polymer848100610.01UniProt (Q9BZJ0)
Pfam (PF02184)
Homo sapiens (Human)Crooked neck homolog,hCrn
11K
(K)
Pre-mRNA-splicing factor SPF27polymer22526163.41UniProt (O75934)
Pfam (PF05700)
Homo sapiens (Human)Breast carcinoma-amplified sequence 2,DNA amplified in mammary carcinoma 1 protein,Spliceosome-associated protein SPF 27
12L
(L)
Cell division cycle 5-like proteinpolymer80292406.91UniProt (Q99459)
Pfam (PF13921)
Pfam (PF11831)
Homo sapiens (Human)Cdc5-like protein,Pombe cdc5-related protein
13M
(M)
Pre-mRNA-splicing factor SYF2polymer24328780.51UniProt (O95926)
Pfam (PF08231)
Homo sapiens (Human)CCNDBP1-interactor,p29
14N
(N)
Protein BUD31 homologpolymer14417032.81UniProt (P41223)
Pfam (PF01125)
Homo sapiens (Human)Protein EDG-2,Protein G10 homolog
15O
(O)
Pre-mRNA-splicing factor RBM22polymer42046959.61UniProt (Q9NW64)
Pfam (PF21369)
Pfam (PF00076)
Homo sapiens (Human)RNA-binding motif protein 22,Zinc finger CCCH domain-containing protein 16
16P
(P)
Spliceosome-associated protein CWC15 homologpolymer22926674.41UniProt (Q9P013)
Pfam (PF04889)
Homo sapiens (Human)
17Q
(Q)
Intron-binding protein aquariuspolymer1485171502.51UniProt (O60306)
Pfam (PF16399)
Pfam (PF21143)
Pfam (PF21144)
Pfam (PF13086)
Pfam (PF13087)
Homo sapiens (Human)Intron-binding protein of 160 kDa,IBP160
18R
(R)
SNW domain-containing protein 1polymer53661770.61UniProt (Q13573)
Pfam (PF02731)
Homo sapiens (Human)Nuclear protein SkiP,Nuclear receptor coactivator NCoA-62,Ski-interacting protein
19S
(S)
Peptidyl-prolyl cis-trans isomerase-like 1polymer16618257.81UniProt (Q9Y3C6)
Pfam (PF00160)
Homo sapiens (Human)PPIase,Rotamase PPIL1
20T
(T)
Pleiotropic regulator 1polymer51457280.81UniProt (O43660)
Pfam (PF00400)
Homo sapiens (Human)
21U
(U)
Serine/arginine repetitive matrix protein 2polymer2752300255.31UniProt (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
22V
(V)
Pre-mRNA-splicing factor CWC22 homologpolymer908105646.61UniProt (Q9HCG8)
Pfam (PF02854)
Pfam (PF02847)
Homo sapiens (Human)Nucampholin homolog,fSAPb
23W
(W)
Pre-mRNA-processing factor 17polymer57965612.21UniProt (O60508)
Pfam (PF00400)
Homo sapiens (Human)Cell division cycle 40 homolog,EH-binding protein 3,Ehb3,PRP17 homolog,hPRP17
24X
(X)
PRKR-interacting protein 1polymer18421040.21UniProt (Q9H875)
Pfam (PF06658)
Homo sapiens (Human)
25Y
(Y)
ATP-dependent RNA helicase DHX8polymer1220139508.31UniProt (Q14562)
Pfam (PF00575)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF04408)
Pfam (PF21010)
Pfam (PF07717)
Homo sapiens (Human)DEAH box protein 8,RNA helicase HRH1
26Z
(Z)
Pre-mRNA-splicing factor SLU7polymer58668510.81UniProt (O95391)
Pfam (PF11708)
Homo sapiens (Human)hSlu7
27AA, HA
(a, h)
Small nuclear ribonucleoprotein Sm D3polymer12613940.32UniProt (P62318)
Pfam (PF01423)
Homo sapiens (Human)Sm-D3,snRNP core protein D3
28BA, IA
(b, i)
Small nuclear ribonucleoprotein-associated proteins B and B'polymer23123686.02UniProt (P14678)
Pfam (PF01423)
Homo sapiens (Human)snRNP-B,Sm protein B/B',SmB/B'
29CA, JA
(c, j)
Small nuclear ribonucleoprotein Sm D1polymer11913310.72UniProt (P62314)
Pfam (PF01423)
Homo sapiens (Human)Sm-D1,Sm-D autoantigen,snRNP core protein D1
30DA, KA
(d, k)
Small nuclear ribonucleoprotein Sm D2polymer11813551.92UniProt (P62316)
Pfam (PF01423)
Homo sapiens (Human)Sm-D2,snRNP core protein D2
31EA, LA
(f, m)
Small nuclear ribonucleoprotein Fpolymer869734.22UniProt (P62306)
Pfam (PF01423)
Homo sapiens (Human)snRNP-F,Sm protein F,SmF
32FA, MA
(e, l)
Small nuclear ribonucleoprotein Epolymer9210817.62UniProt (P62304)
Pfam (PF01423)
Homo sapiens (Human)snRNP-E,Sm protein E,SmE
33GA, NA
(g, n)
Small nuclear ribonucleoprotein Gpolymer768508.12UniProt (P62308)
Pfam (PF01423)
Homo sapiens (Human)snRNP-G,Sm protein G,SmG
34OA
(o)
U2 small nuclear ribonucleoprotein A'polymer25528456.61UniProt (P09661)
Pfam (PF14580)
Homo sapiens (Human)U2 snRNP A'
35PA
(p)
U2 small nuclear ribonucleoprotein B''polymer22525524.41UniProt (P08579)
Pfam (PF00076)
Homo sapiens (Human)U2 snRNP B''
36QA, RA, SA, TA
(q, r, s, t)
Pre-mRNA-processing factor 19polymer50455245.54UniProt (Q9UMS4)
Pfam (PF04564)
Pfam (PF08606)
Pfam (PF00400)
Homo sapiens (Human)Nuclear matrix protein 200,PRP19/PSO4 homolog,hPso4,RING-type E3 ubiquitin transferase PRP19,Senescence evasion factor
37UA
(u)
Eukaryotic initiation factor 4A-IIIpolymer41146931.01UniProt (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
38VA
(v)
Protein mago nashi homolog 2polymer14817301.81UniProt (Q96A72)
Pfam (PF02792)
Homo sapiens (Human)
39WA
(w)
RNA-binding protein 8Apolymer17419925.11UniProt (Q9Y5S9)
Pfam (PF00076)
Homo sapiens (Human)Binder of OVCA1-1,BOV-1,RNA-binding motif protein 8A,RNA-binding protein Y14,Ribonucleoprotein RBM8A
40XA
(x)
Protein CASC3polymer70376382.01UniProt (O15234)
Pfam (PF09405)
Homo sapiens (Human)Cancer susceptibility candidate gene 3 protein,Metastatic lymph node gene 51 protein,MLN 51,Protein barentsz,Btz
41YA
(A)
INOSITOL HEXAKISPHOSPHATEnon-polymer660.01Chemie (IHP)
42ZA
(C)
GUANOSINE-5'-TRIPHOSPHATEnon-polymer523.21Chemie (GTP)
43AB, DB, EB, FB, GB...
(C, D, F, Q, u)
MAGNESIUM IONnon-polymer24.311Chemie (MG)
44BB, CB
(D)
ADENOSINE-5'-DIPHOSPHATEnon-polymer427.22Chemie (ADP)
45KB, LB, MB, NB, OB...
(N, O, Z)
ZINC IONnon-polymer65.47Chemie (ZN)
46QB, VB
(Q, u)
ADENOSINE-5'-TRIPHOSPHATEnon-polymer507.22Chemie (ATP)
Sequence modifications
Y: 1 - 1220 (UniProt: Q14562)
PDBExternal DatabaseDetails
Thr 420Asp 420conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains50
Total formula weight2958303.3
Non-Polymers*Number of molecules24
Total formula weight3777.2
All*Total formula weight2962080.5
*Water molecules are not included.

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PDB entries from 2024-10-30

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