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Cryo-EM Structure of Pre-B+ATP Complex (core part)

Source organism: Homo sapiens
Biochemical function: protein binding
Biological process: RNA splicing
Cellular component: spliceosomal complex

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EC 3.6.4.13: RNA helicase

Reaction catalysed:
ATP + H(2)O = ADP + phosphate
Systematic name:
ATP phosphohydrolase (RNA helix unwinding)
Alternative Name(s):
  • CSFV NS3 helicase
  • DBP2
  • DDX17
  • DDX25
  • DDX3
  • DDX3X
  • DDX3Y
  • DDX4
  • DDX5
  • DEAD-box RNA helicase
  • DEAD-box protein DED1
  • DEAH-box RNA helicase
  • DEAH-box protein 2
  • DED1
  • DbpA
  • Dex(H/D) RNA helicase
  • EIF4A helicase
  • EhDEAD1
  • EhDEAD1 RNA helicase
  • GRTH/DDX25
  • KOKV helicase
  • Mtr4p
  • NPH-II
  • Nonstructural protein 3 helicase
  • RHA
  • RNA helicase A
  • RNA helicase DDX3
  • RNA helicase Hera
  • RNA-dependent ATPase
  • TGBp1 NTPase/helicase domain
  • VRH1

EC 3.4.19.12: Ubiquitinyl hydrolase 1

Reaction catalysed:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Systematic name:
-
Alternative Name(s):
  • Ubiquitin C-terminal hydrolase
  • Ubiquitin carboxyl-terminal hydrolase
  • Ubiquitin thiolesterase
  • Yeast ubiquitin hydrolase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00400
Domain description: WD domain, G-beta repeat
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein Prp4
The deposited structure of PDB entry 8qpb contains 7 copies of Pfam domain PF00400 (WD domain, G-beta repeat) in U4/U6 small nuclear ribonucleoprotein Prp4. Showing 7 copies in chain E [auth F] (this domain is out of the observed residue ranges!).

PF00270
Domain description: DEAD/DEAH box helicase
Occurring in:
  1. U5 small nuclear ribonucleoprotein 200 kDa helicase
  2. Probable ATP-dependent RNA helicase DDX23
The deposited structure of PDB entry 8qpb contains 2 copies of Pfam domain PF00270 (DEAD/DEAH box helicase) in U5 small nuclear ribonucleoprotein 200 kDa helicase. Showing 2 copies in chain A [auth B] (this domain is out of the observed residue ranges!).
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF00270 (DEAD/DEAH box helicase) in Probable ATP-dependent RNA helicase DDX23. Showing 1 copy in chain B [auth G] (this domain is out of the observed residue ranges!).

PF02889
Domain description: Sec63 Brl domain
Occurring in:
  1. U5 small nuclear ribonucleoprotein 200 kDa helicase
The deposited structure of PDB entry 8qpb contains 2 copies of Pfam domain PF02889 (Sec63 Brl domain) in U5 small nuclear ribonucleoprotein 200 kDa helicase. Showing 2 copies in chain A [auth B] (this domain is out of the observed residue ranges!).

PF00271
Domain description: Helicase conserved C-terminal domain
Occurring in:
  1. U5 small nuclear ribonucleoprotein 200 kDa helicase
  2. Probable ATP-dependent RNA helicase DDX23
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF00271 (Helicase conserved C-terminal domain) in U5 small nuclear ribonucleoprotein 200 kDa helicase. Showing 1 copy in chain A [auth B] (this domain is out of the observed residue ranges!).
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF00271 (Helicase conserved C-terminal domain) in Probable ATP-dependent RNA helicase DDX23. Showing 1 copy in chain B [auth G] (this domain is out of the observed residue ranges!).

PF01805
Domain description: Surp module
Occurring in:
  1. Splicing factor 3A subunit 1
The deposited structure of PDB entry 8qpb contains 2 copies of Pfam domain PF01805 (Surp module) in Splicing factor 3A subunit 1. Showing 2 copies in chain N [auth 7] (this domain is out of the observed residue ranges!).

PF00443
Domain description: Ubiquitin carboxyl-terminal hydrolase
Occurring in:
  1. Ubiquitin carboxyl-terminal hydrolase 39
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF00443 (Ubiquitin carboxyl-terminal hydrolase) in Ubiquitin carboxyl-terminal hydrolase 39. Showing 1 copy in chain H [auth U].

PF02148
Domain description: Zn-finger in ubiquitin-hydrolases and other protein
Occurring in:
  1. Ubiquitin carboxyl-terminal hydrolase 39
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF02148 (Zn-finger in ubiquitin-hydrolases and other protein) in Ubiquitin carboxyl-terminal hydrolase 39. Showing 1 copy in chain H [auth U].

PF03343
Domain description: SART-1 family
Occurring in:
  1. U4/U6.U5 tri-snRNP-associated protein 1
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF03343 (SART-1 family) in U4/U6.U5 tri-snRNP-associated protein 1. Showing 1 copy in chain I [auth S].

PF19252
Domain description: HIND motif
Occurring in:
  1. U4/U6.U5 tri-snRNP-associated protein 1
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF19252 (HIND motif) in U4/U6.U5 tri-snRNP-associated protein 1. Showing 1 copy in chain I [auth S] (this domain is out of the observed residue ranges!).

PF13432
Domain description: Tetratricopeptide repeat
Occurring in:
  1. Pre-mRNA-processing factor 6
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF13432 (Tetratricopeptide repeat) in Pre-mRNA-processing factor 6. Showing 1 copy in chain F [auth N] (this domain is out of the observed residue ranges!).

PF14559
Domain description: Tetratricopeptide repeat
Occurring in:
  1. Pre-mRNA-processing factor 6
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF14559 (Tetratricopeptide repeat) in Pre-mRNA-processing factor 6. Showing 1 copy in chain F [auth N] (this domain is out of the observed residue ranges!).

PF06424
Domain description: PRP1 splicing factor, N-terminal
Occurring in:
  1. Pre-mRNA-processing factor 6
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF06424 (PRP1 splicing factor, N-terminal) in Pre-mRNA-processing factor 6. Showing 1 copy in chain F [auth N].

PF01248
Domain description: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Occurring in:
  1. NHP2-like protein 1
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF01248 (Ribosomal protein L7Ae/L30e/S12e/Gadd45 family) in NHP2-like protein 1. Showing 1 copy in chain K [auth M].

PF09785
Domain description: Prp31 C terminal domain
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein Prp31
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF09785 (Prp31 C terminal domain) in U4/U6 small nuclear ribonucleoprotein Prp31. Showing 1 copy in chain D [auth L].

PF01798
Domain description: snoRNA binding domain, fibrillarin
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein Prp31
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF01798 (snoRNA binding domain, fibrillarin) in U4/U6 small nuclear ribonucleoprotein Prp31. Showing 1 copy in chain D [auth L].

PF06544
Domain description: Small nuclear ribonucleoprotein Prp3, C-terminal domain
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein Prp3
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF06544 (Small nuclear ribonucleoprotein Prp3, C-terminal domain) in U4/U6 small nuclear ribonucleoprotein Prp3. Showing 1 copy in chain C [auth J] (this domain is out of the observed residue ranges!).

PF08572
Domain description: pre-mRNA processing factor 3 domain
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein Prp3
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF08572 (pre-mRNA processing factor 3 domain) in U4/U6 small nuclear ribonucleoprotein Prp3. Showing 1 copy in chain C [auth J].

PF01480
Domain description: PWI domain
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein Prp3
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF01480 (PWI domain) in U4/U6 small nuclear ribonucleoprotein Prp3. Showing 1 copy in chain C [auth J] (this domain is out of the observed residue ranges!).

PF08799
Domain description: pre-mRNA processing factor 4 (PRP4) like
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein Prp4
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF08799 (pre-mRNA processing factor 4 (PRP4) like) in U4/U6 small nuclear ribonucleoprotein Prp4. Showing 1 copy in chain E [auth F].

PF02966
Domain description: Mitosis protein DIM1
Occurring in:
  1. Thioredoxin-like protein 4A
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF02966 (Mitosis protein DIM1) in Thioredoxin-like protein 4A. Showing 1 copy in chain L [auth D].

PF00679
Domain description: Elongation factor G C-terminus
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF00679 (Elongation factor G C-terminus) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain J [auth C].

PF03764
Domain description: Elongation factor G, domain IV
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF03764 (Elongation factor G, domain IV) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain J [auth C].

PF14492
Domain description: Elongation Factor G, domain III
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF14492 (Elongation Factor G, domain III) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain J [auth C].

PF03144
Domain description: Elongation factor Tu domain 2
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF03144 (Elongation factor Tu domain 2) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain J [auth C].

PF00009
Domain description: Elongation factor Tu GTP binding domain
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF00009 (Elongation factor Tu GTP binding domain) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain J [auth C].

PF16004
Domain description: 116 kDa U5 small nuclear ribonucleoprotein component N-terminus
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF16004 (116 kDa U5 small nuclear ribonucleoprotein component N-terminus) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain J [auth C] (this domain is out of the observed residue ranges!).

PF18149
Domain description: N-terminal helicase PWI domain
Occurring in:
  1. U5 small nuclear ribonucleoprotein 200 kDa helicase
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF18149 (N-terminal helicase PWI domain) in U5 small nuclear ribonucleoprotein 200 kDa helicase. Showing 1 copy in chain A [auth B] (this domain is out of the observed residue ranges!).

PF21188
Domain description: Pre-mRNA-splicing helicase BRR2 plug domain
Occurring in:
  1. U5 small nuclear ribonucleoprotein 200 kDa helicase
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF21188 (Pre-mRNA-splicing helicase BRR2 plug domain) in U5 small nuclear ribonucleoprotein 200 kDa helicase. Showing 1 copy in chain A [auth B] (this domain is out of the observed residue ranges!).

PF08084
Domain description: PROCT (NUC072) domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF08084 (PROCT (NUC072) domain) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain G [auth A] (this domain is out of the observed residue ranges!).

PF01398
Domain description: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF01398 (JAB1/Mov34/MPN/PAD-1 ubiquitin protease) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain G [auth A] (this domain is out of the observed residue ranges!).

PF12134
Domain description: PRP8 domain IV core
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF12134 (PRP8 domain IV core) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain G [auth A].

PF10596
Domain description: U6-snRNA interacting domain of PrP8
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF10596 (U6-snRNA interacting domain of PrP8) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain G [auth A].

PF10597
Domain description: U5-snRNA binding site 2 of PrP8
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF10597 (U5-snRNA binding site 2 of PrP8) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain G [auth A].

PF10598
Domain description: RNA recognition motif of the spliceosomal PrP8
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF10598 (RNA recognition motif of the spliceosomal PrP8) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain G [auth A].

PF08083
Domain description: PROCN (NUC071) domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF08083 (PROCN (NUC071) domain) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain G [auth A].

PF08082
Domain description: PRO8NT (NUC069), PrP8 N-terminal domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF08082 (PRO8NT (NUC069), PrP8 N-terminal domain) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain G [auth A].

PF00240
Domain description: Ubiquitin family
Occurring in:
  1. Splicing factor 3A subunit 1
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF00240 (Ubiquitin family) in Splicing factor 3A subunit 1. Showing 1 copy in chain N [auth 7] (this domain is out of the observed residue ranges!).

PF12230
Domain description: Pre-mRNA splicing factor PRP21 like protein
Occurring in:
  1. Splicing factor 3A subunit 1
The deposited structure of PDB entry 8qpb contains 1 copy of Pfam domain PF12230 (Pre-mRNA splicing factor PRP21 like protein) in Splicing factor 3A subunit 1. Showing 1 copy in chain N [auth 7].

Rfam RNA families (Rfam)
RF00015
Domain description: U4 spliceosomal RNA
Occurring in:
  1. U4 snRNA
The deposited structure of PDB entry 8qpb contains 1 copy of Rfam domain RF00015 (U4 spliceosomal RNA) in U4 snRNA. Showing 1 copy in chain O [auth 4].

RF00020
Domain description: U5 spliceosomal RNA
Occurring in:
  1. U5 snRNA
The deposited structure of PDB entry 8qpb contains 1 copy of Rfam domain RF00020 (U5 spliceosomal RNA) in U5 snRNA. Showing 1 copy in chain M [auth 5].

RF00026
Domain description: U6 spliceosomal RNA
Occurring in:
  1. U6 snRNA
The deposited structure of PDB entry 8qpb contains 1 copy of Rfam domain RF00026 (U6 spliceosomal RNA) in U6 snRNA. Showing 1 copy in chain P [auth 6].

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