› 8c6j

Electron Microscopy
2.8Å resolution

Human spliceosomal PM5 C* complex

Released:
DOI: 10.2210/pdb8c6j/pdb
PDB entry 8c6j coloured by chain, front view.
PDB entry 8c6j coloured by chain, side view.
PDB entry 8c6j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Regulation of 3' splice site selection after step 1 of splicing by spliceosomal C* proteins.
Dybkov O, Preußner M, El Ayoubi L, Feng VY, Harnisch C, Merz K, Leupold P, Yudichev P, Agafonov DE, Will CL, Girard C, Dienemann C, Urlaub H, Kastner B, Heyd F, Lührmann R
OpenAccess logo Sci Adv 9 eadf1785 (2023)
PMID: 36867703
Related structures: EMD-16452

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
Peptidylproline (omega=180) = peptidylproline (omega=0)
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 63-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-271722 (preferred)
Entry contents:
48 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (53 distinct):
Splicing factor ESS-2 homolog Chain: 4
Molecule details ›
Chain: 4
Length: 476 amino acids
Theoretical weight: 52.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96DF8 (Residues: 1-476; Coverage: 100%)
Gene names: DGCR13, DGCR14, DGSH, DGSI, ES2, ESS2
Sequence domains: Nuclear protein Es2
Eukaryotic initiation factor 4A-III Chain: 7
Molecule details ›
Chain: 7
Length: 411 amino acids
Theoretical weight: 46.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P38919 (Residues: 1-411; Coverage: 100%)
Gene names: DDX48, EIF4A3, KIAA0111
Sequence domains:
RNA-binding protein 8A Chain: 8
Molecule details ›
Chain: 8
Length: 174 amino acids
Theoretical weight: 19.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y5S9 (Residues: 1-174; Coverage: 100%)
Gene names: HSPC114, MDS014, RBM8, RBM8A
Sequence domains: RNA recognition motif
Protein mago nashi homolog Chain: 9
Molecule details ›
Chain: 9
Length: 146 amino acids
Theoretical weight: 17.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61326 (Residues: 1-146; Coverage: 100%)
Gene names: MAGOH, MAGOHA
Sequence domains: Mago nashi protein
Pre-mRNA-processing-splicing factor 8 Chain: A
Molecule details ›
Chain: A
Length: 2335 amino acids
Theoretical weight: 273.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P2Q9 (Residues: 1-2335; Coverage: 100%)
Gene names: PRPC8, PRPF8
Sequence domains:
U5 small nuclear ribonucleoprotein 200 kDa helicase Chain: B
Molecule details ›
Chain: B
Length: 2136 amino acids
Theoretical weight: 244.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75643 (Residues: 1-2136; Coverage: 100%)
Gene names: ASCC3L1, BRR2, HELIC2, KIAA0788, SNRNP200
Sequence domains:
116 kDa U5 small nuclear ribonucleoprotein component Chain: C
Molecule details ›
Chain: C
Length: 972 amino acids
Theoretical weight: 109.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15029 (Residues: 1-972; Coverage: 100%)
Gene names: EFTUD2, KIAA0031, SNRP116
Sequence domains:
Peptidyl-prolyl cis-trans isomerase-like 3 Chain: C3
Molecule details ›
Chain: C3
Length: 161 amino acids
Theoretical weight: 18.18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H2H8 (Residues: 1-161; Coverage: 100%)
Gene name: PPIL3
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Probable ATP-dependent RNA helicase DDX41 Chain: CD
Molecule details ›
Chain: CD
Length: 622 amino acids
Theoretical weight: 69.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UJV9 (Residues: 1-622; Coverage: 100%)
Gene names: ABS, DDX41
Sequence domains:
Peptidyl-prolyl cis-trans isomerase E Chain: CE
Molecule details ›
Chain: CE
Length: 301 amino acids
Theoretical weight: 33.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UNP9 (Residues: 1-301; Coverage: 100%)
Gene names: CYP33, PPIE
Sequence domains:
Protein FAM50A Chain: CF
Molecule details ›
Chain: CF
Length: 339 amino acids
Theoretical weight: 40.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14320 (Residues: 1-339; Coverage: 100%)
Gene names: DXS9928E, FAM50A, HXC26, XAP5
Sequence domains: XAP5, circadian clock regulator C-terminal domain
Pre-mRNA-splicing factor ISY1 homolog Chain: CI
Molecule details ›
Chain: CI
Length: 285 amino acids
Theoretical weight: 33.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9ULR0 (Residues: 1-285; Coverage: 100%)
Gene names: ISY1, KIAA1160
Sequence domains: Isy1-like splicing family
Nitric oxide synthase-interacting protein Chain: CN
Molecule details ›
Chain: CN
Length: 301 amino acids
Theoretical weight: 33.22 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y314 (Residues: 1-301; Coverage: 100%)
Gene names: CGI-25, NOSIP
Sequence domains: Zinc-finger of nitric oxide synthase-interacting protein
Splicing factor C9orf78 Chain: CT
Molecule details ›
Chain: CT
Length: 289 amino acids
Theoretical weight: 33.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NZ63 (Residues: 1-289; Coverage: 100%)
Gene names: C9orf78, HCA59
Sequence domains: Hepatocellular carcinoma-associated antigen 59
PRKR-interacting protein 1 Chain: D
Molecule details ›
Chain: D
Length: 184 amino acids
Theoretical weight: 21.04 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H875 (Residues: 1-184; Coverage: 100%)
Gene name: PRKRIP1
Sequence domains: Protein of unknown function (DUF1168)
Splicing factor Cactin Chain: F
Molecule details ›
Chain: F
Length: 758 amino acids
Theoretical weight: 88.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WUQ7 (Residues: 1-758; Coverage: 100%)
Gene names: C19orf29, CACTIN
Sequence domains:
Protein FAM32A Chain: G
Molecule details ›
Chain: G
Length: 112 amino acids
Theoretical weight: 13.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y421 (Residues: 1-112; Coverage: 100%)
Gene names: CGI-144, FAM32A, OTAG12
Sequence domains: FAM32A
Pre-mRNA-splicing factor CWC22 homolog Chain: H
Molecule details ›
Chain: H
Length: 500 amino acids
Theoretical weight: 57.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9HCG8 (Residues: 149-648; Coverage: 55%)
Gene names: CWC22, KIAA1604, NCM
Sequence domains:
Pleiotropic regulator 1 Chain: J
Molecule details ›
Chain: J
Length: 514 amino acids
Theoretical weight: 57.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43660 (Residues: 1-514; Coverage: 100%)
Gene name: PLRG1
Sequence domains: WD domain, G-beta repeat
SNW domain-containing protein 1 Chain: K
Molecule details ›
Chain: K
Length: 536 amino acids
Theoretical weight: 61.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13573 (Residues: 1-536; Coverage: 100%)
Gene names: SKIIP, SKIP, SNW1
Sequence domains: SKIP/SNW domain
Protein BUD31 homolog Chain: L
Molecule details ›
Chain: L
Length: 144 amino acids
Theoretical weight: 17.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P41223 (Residues: 1-144; Coverage: 100%)
Gene names: BUD31, EDG2
Sequence domains: Pre-mRNA-splicing factor BUD31
Pre-mRNA-splicing factor RBM22 Chain: M
Molecule details ›
Chain: M
Length: 420 amino acids
Theoretical weight: 46.96 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NW64 (Residues: 1-420; Coverage: 100%)
Gene names: 199G4, RBM22, ZC3H16
Sequence domains:
U5 small nuclear ribonucleoprotein 40 kDa protein Chain: N
Molecule details ›
Chain: N
Length: 357 amino acids
Theoretical weight: 39.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96DI7 (Residues: 1-357; Coverage: 100%)
Gene names: PRP8BP, SFP38, SNRNP40, WDR57
Sequence domains: WD domain, G-beta repeat
Cell division cycle 5-like protein Chain: O
Molecule details ›
Chain: O
Length: 802 amino acids
Theoretical weight: 92.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99459 (Residues: 1-802; Coverage: 100%)
Gene names: CDC5L, KIAA0432, PCDC5RP
Sequence domains:
Spliceosome-associated protein CWC15 homolog Chain: P
Molecule details ›
Chain: P
Length: 229 amino acids
Theoretical weight: 26.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P013 (Residues: 1-229; Coverage: 100%)
Gene names: AD-002, C11orf5, CWC15, HSPC148
Sequence domains: Cwf15/Cwc15 cell cycle control protein
Serine/arginine repetitive matrix protein 2 Chain: R
Molecule details ›
Chain: R
Length: 2752 amino acids
Theoretical weight: 300.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UQ35 (Residues: 1-2752; Coverage: 100%)
Gene names: HSPC075, KIAA0324, SRL300, SRM300, SRRM2
Sequence domains: cwf21 domain
Crooked neck-like protein 1 Chain: S
Molecule details ›
Chain: S
Length: 687 amino acids
Theoretical weight: 83.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BZJ0 (Residues: 162-848; Coverage: 81%)
Gene names: CGI-201, CRN, CRNKL1, MSTP021
Sequence domains: HAT (Half-A-TPR) repeat
Pre-mRNA-splicing factor SYF1 Chain: T
Molecule details ›
Chain: T
Length: 855 amino acids
Theoretical weight: 100.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9HCS7 (Residues: 1-855; Coverage: 100%)
Gene names: HCNP, KIAA1177, PP3898, SYF1, XAB2
Sequence domains: Tetratricopeptide repeat
RNA helicase aquarius Chain: U
Molecule details ›
Chain: U
Length: 1485 amino acids
Theoretical weight: 171.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60306 (Residues: 1-1485; Coverage: 100%)
Gene names: AQR, KIAA0560
Sequence domains:
ATP-dependent RNA helicase DHX8 Chain: V
Molecule details ›
Chain: V
Length: 1220 amino acids
Theoretical weight: 139.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14562 (Residues: 1-1220; Coverage: 100%)
Gene names: DDX8, DHX8
Sequence domains:
U2 small nuclear ribonucleoprotein A' Chain: W
Molecule details ›
Chain: W
Length: 255 amino acids
Theoretical weight: 28.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09661 (Residues: 1-255; Coverage: 100%)
Gene name: SNRPA1
Sequence domains: Leucine-rich repeat
U2 small nuclear ribonucleoprotein B'' Chain: Y
Molecule details ›
Chain: Y
Length: 225 amino acids
Theoretical weight: 25.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08579 (Residues: 1-225; Coverage: 100%)
Gene name: SNRPB2
Sequence domains: RNA recognition motif
NF-kappa-B-activating protein Chain: Z
Molecule details ›
Chain: Z
Length: 415 amino acids
Theoretical weight: 47.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N5F7 (Residues: 1-415; Coverage: 100%)
Gene name: NKAP
Sequence domains:
Small nuclear ribonucleoprotein Sm D2 Chains: a, m
Molecule details ›
Chains: a, m
Length: 118 amino acids
Theoretical weight: 13.55 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62316 (Residues: 1-118; Coverage: 100%)
Gene names: SNRPD1, SNRPD2
Sequence domains: LSM domain
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: b, k
Molecule details ›
Chains: b, k
Length: 240 amino acids
Theoretical weight: 24.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P14678 (Residues: 1-240; Coverage: 100%)
Gene names: COD, SNRPB, SNRPB1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: c, l
Molecule details ›
Chains: c, l
Length: 119 amino acids
Theoretical weight: 13.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62314 (Residues: 1-119; Coverage: 100%)
Gene name: SNRPD1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D3 Chains: d, n
Molecule details ›
Chains: d, n
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62318 (Residues: 1-126; Coverage: 100%)
Gene name: SNRPD3
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chains: e, p
Molecule details ›
Chains: e, p
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62304 (Residues: 1-92; Coverage: 100%)
Gene name: SNRPE
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chains: f, q
Molecule details ›
Chains: f, q
Length: 86 amino acids
Theoretical weight: 9.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62306 (Residues: 1-86; Coverage: 100%)
Gene names: PBSCF, SNRPF
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chains: g, r
Molecule details ›
Chains: g, r
Length: 76 amino acids
Theoretical weight: 8.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62308 (Residues: 1-76; Coverage: 100%)
Gene names: PBSCG, SNRPG
Sequence domains: LSM domain
Pre-mRNA-splicing factor SLU7 Chain: h
Molecule details ›
Chain: h
Length: 586 amino acids
Theoretical weight: 68.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95391 (Residues: 1-586; Coverage: 100%)
Gene name: SLU7
Sequence domains: Pre-mRNA splicing Prp18-interacting factor
Peptidyl-prolyl cis-trans isomerase-like 1 Chain: i
Molecule details ›
Chain: i
Length: 166 amino acids
Theoretical weight: 18.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3C6 (Residues: 1-166; Coverage: 100%)
Gene names: CGI-124, CYPL1, PPIL1, UNQ2425/PRO4984
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
STING ER exit protein Chain: j
Molecule details ›
Chain: j
Length: 222 amino acids
Theoretical weight: 25.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H5V9 (Residues: 1-222; Coverage: 100%)
Gene names: CXorf56, STEEP1
Pre-mRNA-processing factor 17 Chain: o
Molecule details ›
Chain: o
Length: 579 amino acids
Theoretical weight: 65.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60508 (Residues: 1-579; Coverage: 100%)
Gene names: CDC40, EHB3, PRP17, PRPF17
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-splicing factor SPF27 Chain: s
Molecule details ›
Chain: s
Length: 225 amino acids
Theoretical weight: 26.16 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75934 (Residues: 1-225; Coverage: 100%)
Gene names: BCAS2, DAM1
Sequence domains: Breast carcinoma amplified sequence 2 (BCAS2)
Pre-mRNA-processing factor 19 Chains: t, u, v, w
Molecule details ›
Chains: t, u, v, w
Length: 504 amino acids
Theoretical weight: 55.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UMS4 (Residues: 1-504; Coverage: 100%)
Gene names: NMP200, PRP19, PRPF19, SNEV
Sequence domains:
Pre-mRNA-splicing factor SYF2 Chain: y
Molecule details ›
Chain: y
Length: 243 amino acids
Theoretical weight: 28.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95926 (Residues: 1-243; Coverage: 100%)
Gene names: CBPIN, GCIPIP, SYF2
Sequence domains: SYF2 splicing factor
Splicing regulator SDE2 Chain: z
Molecule details ›
Chain: z
Length: 451 amino acids
Theoretical weight: 49.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6IQ49 (Residues: 1-451; Coverage: 100%)
Gene names: C1orf55, SDE2
Sequence domains:
U2 snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA
U5 snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 116 nucleotides
Theoretical weight: 36.91 KDa
Sequence domains: U5 spliceosomal RNA
U6 snRNA Chain: 6
Molecule details ›
Chain: 6
Length: 106 nucleotides
Theoretical weight: 34.1 KDa
Sequence domains: U6 spliceosomal RNA
PM5 5' Exon Chain: E
Molecule details ›
Chain: E
Length: 242 nucleotides
Theoretical weight: 78.46 KDa
PM5 Intron Chain: I
Molecule details ›
Chain: I
Length: 235 nucleotides
Theoretical weight: 74.97 KDa

Ligands and Environments

6 bound ligands:
Ligand K 2 x K
Ligand MG 7 x MG
Ligand ATP 1 x ATP
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand ZN 6 x ZN
1 modified residue:
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-16452

Quick links

Citations

4 citation in other articles

Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome.
Norppa et al. (2024)
3 more

1 mention without citation

Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage.
Osterhoudt et al. (2024)