5YZG image
Deposition Date 2017-12-14
Release Date 2018-08-08
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5YZG
Keywords:
SPLICING
Title:
The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5YZG validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans iso
Gene (Uniprot):PPIE
Chain IDs:ZA (auth: 1)
Chain Length:301
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UNP9 Pfam ID:PF00076, PF00160 EC:5.2.1.8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptidylprolyl isomerase doma
Gene (Uniprot):PPWD1
Chain IDs:AB (auth: 2)
Chain Length:646
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96BP3 Pfam ID:PF00400, PF00160 EC:5.2.1.8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans iso
Gene (Uniprot):PPIG
Chain IDs:BB (auth: 3)
Chain Length:754
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13427 Pfam ID:PF00160 EC:5.2.1.8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:UNKNOW
Chain IDs:CB (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing-splicing
Gene (Uniprot):PRPF8
Chain IDs:A
Chain Length:126
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P2Q9 Pfam ID:PF08082, PF08083, PF10598, PF10597, PF10596, PF12134, PF01398, PF08084
Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:B
Chain Length:229
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:116 kDa U5 small nuclear ribo
Gene (Uniprot):EFTUD2
Chain IDs:C
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15029 Pfam ID:PF00009, PF03144, PF16004, PF14492, PF03764, PF00679
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U5 small nuclear ribonucleopr
Gene (Uniprot):SNRNP200
Chain IDs:D
Chain Length:2136
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75643 Pfam ID:PF18149, PF00270, PF02889, PF21188, PF00271, PF23445 EC:3.6.4.13
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U5 small nuclear ribonucleopr
Gene (Uniprot):SNRNP40
Chain IDs:E
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96DI7 Pfam ID:PF00400
Polymer Type:polyribonucleotide
Molecule:U6 snRNA
Chain IDs:F
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:Pre-mRNA
Chain IDs:G
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U2 snRNA
Chain IDs:H
Chain Length:126
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SYF1
Gene (Uniprot):XAB2
Chain IDs:I
Chain Length:229
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9HCS7 Pfam ID:PF13181, PF23233, PF23220, PF23231
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Crooked neck-like protein 1
Gene (Uniprot):CRNKL1
Chain IDs:J
Chain Length:848
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BZJ0 Pfam ID:PF02184, PF23231
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SPF2
Gene (Uniprot):BCAS2
Chain IDs:K
Chain Length:225
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75934 Pfam ID:PF05700
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cell division cycle 5-like pr
Gene (Uniprot):CDC5L
Chain IDs:L
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q99459 Pfam ID:PF13921, PF11831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SYF2
Gene (Uniprot):SYF2
Chain IDs:N (auth: M)
Chain Length:243
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O95926 Pfam ID:PF08231
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein BUD31 homolog
Gene (Uniprot):BUD31
Chain IDs:O (auth: N)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P41223 Pfam ID:PF01125
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor RBM2
Gene (Uniprot):RBM22
Chain IDs:P (auth: O)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NW64 Pfam ID:PF21369, PF00076, PF25584
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spliceosome-associated protei
Gene (Uniprot):CWC15
Chain IDs:Q (auth: P)
Chain Length:229
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9P013 Pfam ID:PF04889
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Intron-binding protein aquari
Gene (Uniprot):AQR
Chain IDs:U (auth: Q)
Chain Length:1485
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O60306 Pfam ID:PF21143, PF13086, PF16399, PF21144, PF13087 EC:3.6.4.13
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SNW domain-containing protein
Gene (Uniprot):SNW1
Chain IDs:R
Chain Length:536
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13573 Pfam ID:PF02731
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans iso
Gene (Uniprot):PPIL1
Chain IDs:S
Chain Length:504
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3C6 Pfam ID:PF00160 EC:5.2.1.8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pleiotropic regulator 1
Gene (Uniprot):PLRG1
Chain IDs:T
Chain Length:504
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O43660 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Serine/arginine repetitive ma
Gene (Uniprot):SRRM2
Chain IDs:V (auth: U)
Chain Length:2752
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UQ35 Pfam ID:PF08312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CWC2
Gene (Uniprot):CWC22
Chain IDs:W (auth: V)
Chain Length:908
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9HCG8 Pfam ID:PF02854, PF02847
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 17
Gene (Uniprot):CDC40
Chain IDs:X (auth: W)
Chain Length:579
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O60508 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CWC2
Gene (Uniprot):CWC25
Chain IDs:Y (auth: X)
Chain Length:703
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NXE8 Pfam ID:PF10197, PF12542
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Coiled-coil domain-containing
Gene (Uniprot):YJU2
Chain IDs:Z (auth: Y)
Chain Length:323
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BW85 Pfam ID:PF04502
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor ATP-
Gene (Uniprot):DHX38
Chain IDs:AA (auth: Z)
Chain Length:1227
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92620 Pfam ID:PF00270, PF00271, PF04408, PF21010, PF07717 EC:3.6.4.13
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPD3
Chain IDs:JA (auth: h), SA (auth: a)
Chain Length:126
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62318 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPB
Chain IDs:KA (auth: i), TA (auth: b)
Chain Length:229
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P14678 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPD1
Chain IDs:LA (auth: j), UA (auth: c)
Chain Length:848
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62314 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPD2
Chain IDs:MA (auth: k), VA (auth: d)
Chain Length:2136
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62316 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPE
Chain IDs:OA (auth: l), XA (auth: e)
Chain Length:92
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62304 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPF
Chain IDs:NA (auth: m), WA (auth: f)
Chain Length:243
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62306 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SNRPG
Chain IDs:PA (auth: n), YA (auth: g)
Chain Length:76
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62308 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 small nuclear ribonucleopr
Gene (Uniprot):SNRPA1
Chain IDs:QA (auth: o)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P09661 Pfam ID:PF14580
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 small nuclear ribonucleopr
Gene (Uniprot):SNRPB2
Chain IDs:RA (auth: p)
Chain Length:229
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P08579 Pfam ID:PF00076
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 19
Gene (Uniprot):PRPF19
Chain IDs:BA (auth: q), CA (auth: r), DA (auth: s), EA (auth: t)
Chain Length:504
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:Q9UMS4 Pfam ID:PF04564, PF08606, PF00400, PF24814 EC:2.3.2.27
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic initiation factor
Gene (Uniprot):EIF4A3
Chain IDs:FA (auth: u)
Chain Length:2752
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P38919 Pfam ID:PF00270, PF00271 EC:3.6.4.13
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein mago nashi homolog 2
Gene (Uniprot):MAGOHB
Chain IDs:GA (auth: v)
Chain Length:908
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96A72 Pfam ID:PF02792
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA-binding protein 8A
Gene (Uniprot):RBM8A
Chain IDs:HA (auth: w)
Chain Length:579
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y5S9 Pfam ID:PF00076
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein CASC3
Gene (Uniprot):CASC3
Chain IDs:IA (auth: x)
Chain Length:703
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15234 Pfam ID:PF09405
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor ISY1
Gene (Uniprot):ISY1
Chain IDs:M (auth: y)
Chain Length:323
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9ULR0 Pfam ID:PF06246
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP R SER modified residue
Ligand Molecules
ADP
ATP
GTP
IHP
MG
ZN
Primary Citation
Structure of a human catalytic step I spliceosome
Science 359 537 545 (2018)
PMID: 29301961 DOI: 10.1126/science.aar6401

Abstact

Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron microscopy structure of the human C complex at an average resolution of 4.1 angstroms. Compared with the Saccharomyces cerevisiae C complex, the human complex contains 11 additional proteins. The step I splicing factors CCDC49 and CCDC94 (Cwc25 and Yju2 in S. cerevisiae, respectively) closely interact with the DEAH-family adenosine triphosphatase/helicase Prp16 and bridge the gap between Prp16 and the active-site RNA elements. These features, together with structural comparison of the human C and C* complexes, provide mechanistic insights into ribonucleoprotein remodeling and allow the proposition of a working mechanism for the C-to-C* transition.

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Protein

Chemical

Disease

Primary Citation of related structures
5YZG
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