PDBe 6ahd

Electron Microscopy
3.8Å resolution

The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution

Released:
Source organism: Homo sapiens
Related structures: EMD-9624

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 63-mer (preferred)
Entry contents:
44 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (49 distinct):
Pre-mRNA-processing-splicing factor 8 Chain: A
Thioredoxin-like protein 4A Chain: O
Molecule details ›
Chain: O
Length: 142 amino acids
Theoretical weight: 16.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P83876 (Residues: 1-142; Coverage: 100%)
Gene names: DIM1, TXNL4, TXNL4A
Sequence domains: Mitosis protein DIM1
116 kDa U5 small nuclear ribonucleoprotein component Chain: C
Pre-mRNA-processing factor 6 Chain: N
Molecule details ›
Chain: N
Length: 941 amino acids
Theoretical weight: 107.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O94906 (Residues: 1-941; Coverage: 100%)
Gene names: C20orf14, PRPF6
Sequence domains:
NHP2-like protein 1 Chain: M
Molecule details ›
Chain: M
Length: 128 amino acids
Theoretical weight: 14.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55769 (Residues: 1-128; Coverage: 100%)
Gene names: NHP2L1, SNU13
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
U4/U6 small nuclear ribonucleoprotein Prp31 Chain: L
Molecule details ›
Chain: L
Length: 499 amino acids
Theoretical weight: 55.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WWY3 (Residues: 1-499; Coverage: 100%)
Gene names: PRP31, PRPF31
Sequence domains:
U4/U6.U5 tri-snRNP-associated protein 1 Chain: 9
Molecule details ›
Chain: 9
Length: 800 amino acids
Theoretical weight: 90.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43290 (Residues: 1-800; Coverage: 100%)
Gene name: SART1
Sequence domains: SART-1 family
U4/U6 small nuclear ribonucleoprotein Prp3 Chain: J
Molecule details ›
Chain: J
Length: 683 amino acids
Theoretical weight: 77.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43395 (Residues: 1-683; Coverage: 100%)
Gene names: HPRP3, PRP3, PRPF3
Sequence domains:
SmB Chains: U, a, i
Molecule details ›
Chains: U, a, i
Length: 231 amino acids
Theoretical weight: 23.69 KDa
Source organism: Homo sapiens
Small nuclear ribonucleoprotein Sm D1 Chains: V, b, j
Molecule details ›
Chains: V, b, j
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 D2 Chains: P, c, k
Molecule details ›
Chains: P, c, k
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
SmE Chains: Q, d, l
Molecule details ›
Chains: Q, d, l
Length: 86 amino acids
Theoretical weight: 9.73 KDa
Source organism: Homo sapiens
SmF Chains: R, e, m
Molecule details ›
Chains: R, e, m
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Homo sapiens
Small nuclear ribonucleoprotein G Chains: S, f, n
Molecule details ›
Chains: S, f, n
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
Small nuclear ribonucleoprotein Sm D3 Chains: T, g, h
Molecule details ›
Chains: T, g, h
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
U5 small nuclear ribonucleoprotein 40 kDa protein Chain: E
Molecule details ›
Chain: E
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
WW domain-binding protein 4 Chain: X
Molecule details ›
Chain: X
Length: 376 amino acids
Theoretical weight: 42.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75554 (Residues: 1-376; Coverage: 100%)
Gene names: FBP21, FNBP21, WBP4
Sequence domains:
Peptidyl-prolyl cis-trans isomerase H Chain: W
Molecule details ›
Chain: W
Length: 177 amino acids
Theoretical weight: 19.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43447 (Residues: 1-177; Coverage: 100%)
Gene names: CYP20, CYPH, PPIH
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Ubiquitin-like protein 5 Chain: A0
Molecule details ›
Chain: A0
Length: 73 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BZL1 (Residues: 1-73; Coverage: 100%)
Gene name: UBL5
Sequence domains: Ubiquitin family
Microfibrillar-associated protein 1 Chain: 0
Molecule details ›
Chain: 0
Length: 439 amino acids
Theoretical weight: 52.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55081 (Residues: 1-439; Coverage: 100%)
Gene name: MFAP1
Sequence domains: Microfibril-associated/Pre-mRNA processing
Pre-mRNA-splicing factor 38A Chain: Z
Molecule details ›
Chain: Z
Length: 312 amino acids
Theoretical weight: 37.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8NAV1 (Residues: 1-312; Coverage: 100%)
Gene name: PRPF38A
Sequence domains:
Zinc finger matrin-type protein 2 Chain: 8
Molecule details ›
Chain: 8
Length: 199 amino acids
Theoretical weight: 23.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96NC0 (Residues: 1-199; Coverage: 100%)
Gene name: ZMAT2
Sequence domains: Zinc-finger double-stranded RNA-binding
WD40 repeat-containing protein SMU1 Chain: Y
Molecule details ›
Chain: Y
Length: 513 amino acids
Theoretical weight: 57.62 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q2TAY7 (Residues: 1-513; Coverage: 100%)
Gene name: SMU1
Sequence domains:
U2 small nuclear ribonucleoprotein A' Chain: o
Molecule details ›
Chain: o
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: p
Molecule details ›
Chain: p
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. (a.k.a. RRM, RBD, or RNP domain)
Splicing factor 3A subunit 1 Chain: u
Molecule details ›
Chain: u
Length: 793 amino acids
Theoretical weight: 88.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15459 (Residues: 1-793; Coverage: 100%)
Gene names: SAP114, SF3A1
Sequence domains:
Splicing factor 3A subunit 2 Chain: v
Molecule details ›
Chain: v
Length: 464 amino acids
Theoretical weight: 49.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15428 (Residues: 1-464; Coverage: 100%)
Gene names: SAP62, SF3A2
Sequence domains:
Splicing factor 3A subunit 3 Chain: w
Molecule details ›
Chain: w
Length: 501 amino acids
Theoretical weight: 58.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q12874 (Residues: 1-501; Coverage: 100%)
Gene names: SAP61, SF3A3
Sequence domains:
U6 snRNA-associated Sm-like protein LSm2 Chain: q
Molecule details ›
Chain: q
Length: 95 amino acids
Theoretical weight: 10.85 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y333 (Residues: 1-95; Coverage: 100%)
Gene names: C6orf28, G7B, LSM2
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm3 Chain: r
Molecule details ›
Chain: r
Length: 102 amino acids
Theoretical weight: 11.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62310 (Residues: 1-102; Coverage: 100%)
Gene names: LSM3, MDS017
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm4 Chain: s
Molecule details ›
Chain: s
Length: 139 amino acids
Theoretical weight: 15.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y4Z0 (Residues: 1-139; Coverage: 100%)
Gene name: LSM4
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm5 Chain: t
Molecule details ›
Chain: t
Length: 91 amino acids
Theoretical weight: 9.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y4Y9 (Residues: 1-91; Coverage: 100%)
Gene name: LSM5
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm6 Chain: x
Molecule details ›
Chain: x
Length: 80 amino acids
Theoretical weight: 9.14 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62312 (Residues: 1-80; Coverage: 100%)
Gene name: LSM6
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm7 Chain: y
Molecule details ›
Chain: y
Length: 103 amino acids
Theoretical weight: 11.62 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UK45 (Residues: 1-103; Coverage: 100%)
Gene name: LSM7
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm8 Chain: z
Molecule details ›
Chain: z
Length: 96 amino acids
Theoretical weight: 10.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95777 (Residues: 1-96; Coverage: 100%)
Gene name: LSM8
Sequence domains: LSM domain
U4/U6 small nuclear ribonucleoprotein Prp4 Chain: K
Molecule details ›
Chain: K
Length: 522 amino acids
Theoretical weight: 58.54 KDa
Source organism: Homo sapiens
Splicing factor 3B subunit 1 Chain: 1
Molecule details ›
Chain: 1
Length: 1304 amino acids
Theoretical weight: 146.02 KDa
Source organism: Homo sapiens
Splicing factor 3B subunit 3 Chain: 3
Molecule details ›
Chain: 3
Length: 1217 amino acids
Theoretical weight: 135.72 KDa
Source organism: Homo sapiens
SF3b14a, Splicing factor 3B subunit 6 Chain: 5
Molecule details ›
Chain: 5
Length: 125 amino acids
Theoretical weight: 14.61 KDa
Source organism: Homo sapiens
PHD finger-like domain-containing protein 5A Chain: 6
Molecule details ›
Chain: 6
Length: 110 amino acids
Theoretical weight: 12.43 KDa
Source organism: Homo sapiens
Splicing factor 3B subunit 5 Chain: 7
Molecule details ›
Chain: 7
Length: 86 amino acids
Theoretical weight: 10.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BWJ5 (Residues: 1-86; Coverage: 100%)
Gene names: SF3B10, SF3B5
Sequence domains: Splicing factor 3B subunit 10 (SF3b10)
SF3b145, Splicing factor 3B subunit 2 Chain: 2
Molecule details ›
Chain: 2
Length: 895 amino acids
Theoretical weight: 100.38 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: O75533-2 (Residues: 6-103, 104-106, 107-138)
SF3b49, Splicing factor 3B subunit 4 Chain: 4
Molecule details ›
Chain: 4
Length: 424 amino acids
Theoretical weight: 44.44 KDa
Source organism: Homo sapiens
Brr2, U5 small nuclear ribonucleoprotein 200 kDa helicase Chain: D
Molecule details ›
Chain: D
Length: 2136 amino acids
Theoretical weight: 244.82 KDa
Source organism: Homo sapiens
U4snRNA Chain: I
Molecule details ›
Chain: I
Length: 144 nucleotides
Theoretical weight: 46.18 KDa
Sequence domains: U4 spliceosomal RNA
U5snRNA Chain: B
Molecule details ›
Chain: B
Length: 117 nucleotides
Theoretical weight: 37.25 KDa
Sequence domains: U5 spliceosomal RNA
U6snRNA Chain: F
Molecule details ›
Chain: F
Length: 107 nucleotides
Theoretical weight: 34.4 KDa
Sequence domains: U6 spliceosomal RNA
pre-mRNA Chain: G
Molecule details ›
Chain: G
Length: 274 nucleotides
Theoretical weight: 87.89 KDa
U2snRNA Chain: H
Molecule details ›
Chain: H
Length: 188 nucleotides
Theoretical weight: 60.19 KDa
Sequence domains: U2 spliceosomal RNA

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-9624