› 6tbm

Electron Microscopy
20Å resolution

Structure of SAGA bound to TBP, including Spt8 and DUB

Released:
DOI: 10.2210/pdb6tbm/pdb
PDB entry 6tbm coloured by chain, front view.
PDB entry 6tbm coloured by chain, side view.
PDB entry 6tbm coloured by chain, top view.
Source organisms:
Primary publication:
Structure of SAGA and mechanism of TBP deposition on gene promoters.
Papai G, Frechard A, Kolesnikova O, Crucifix C, Schultz P, Ben-Shem A
Nature 577 711-716 (2020)
PMID: 31969704
Related structures: EMD-10446

Function and Biology Details

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).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-111375 (preferred)
Entry contents:
18 distinct polypeptide molecules
Macromolecules (18 distinct):
TATA-box-binding protein Chain: M
Molecule details ›
Chain: M
Length: 240 amino acids
Theoretical weight: 27.04 KDa
Source organism: Komagataella phaffii GS115
Expression system: Escherichia coli
UniProt:
  • Canonical: P13393 (Residues: 1-240; Coverage: 100%)
Gene names: BTF1, SPT15, TBP1, YER148W
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
Transcriptional coactivator HFI1/ADA1 Chain: A
Molecule details ›
Chain: A
Length: 448 amino acids
Theoretical weight: 49.89 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QZA3 (Residues: 1-448; Coverage: 100%)
Gene name: PAS_FragB_0044
Sequence domains: Transcriptional regulator of RNA polII, SAGA, subunit
SCA7 domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 698 amino acids
Theoretical weight: 80 KDa
Source organism: Komagataella phaffii GS115
Expression system: Escherichia coli
UniProt:
  • Canonical: C4QZ39 (Residues: 1-644; Coverage: 100%)
Gene name: PAS_chr1-4_0651
Sequence domains: SCA7, zinc-binding domain
Spt20-like SEP domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 517 amino acids
Theoretical weight: 59.53 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QZ05 (Residues: 1-517; Coverage: 100%)
Gene name: PAS_chr1-4_0620
Sequence domains: Spt20, SEP domain
Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act Chain: D
Molecule details ›
Chain: D
Length: 341 amino acids
Theoretical weight: 39.03 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R3E4 (Residues: 1-341; Coverage: 100%)
Gene name: PAS_chr3_0051
Sequence domains: Transcription initiation factor IID, 18kD subunit
Bromo domain-containing protein Chain: E
Molecule details ›
Chain: E
Length: 1191 amino acids
Theoretical weight: 136.77 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R5C7 (Residues: 1-1191; Coverage: 100%)
Gene name: PAS_chr3_0713
Sequence domains: Bromodomain
Transcription initiation factor TFIID subunit 10 Chain: J
Molecule details ›
Chain: J
Length: 217 amino acids
Theoretical weight: 23.88 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QXP2 (Residues: 1-217; Coverage: 100%)
Gene name: PAS_chr1-4_0182
Sequence domains: Transcription initiation factor TFIID 23-30kDa subunit
Transcription initiation factor TFIID subunit 12 Chain: K
Molecule details ›
Chain: K
Length: 609 amino acids
Theoretical weight: 66.69 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R150 (Residues: 1-609; Coverage: 100%)
Gene name: PAS_chr2-1_0588
Sequence domains: Transcription initiation factor TFIID subunit A
Transcription initiation factor TFIID subunit 5 Chain: G
Molecule details ›
Chain: G
Length: 722 amino acids
Theoretical weight: 80.93 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R4L4 (Residues: 1-722; Coverage: 100%)
Gene name: PAS_chr3_0453
Sequence domains:
TATA box binding protein associated factor (TAF) histone-like fold domain-containing protein Chain: H
Molecule details ›
Chain: H
Length: 485 amino acids
Theoretical weight: 54.89 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QW33 (Residues: 1-485; Coverage: 100%)
Gene name: PAS_chr1-1_0095
Sequence domains:
Transcription initiation factor TFIID subunit 9 Chain: I
Molecule details ›
Chain: I
Length: 153 amino acids
Theoretical weight: 17.3 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QZS5 (Residues: 1-153; Coverage: 100%)
Gene name: PAS_chr2-1_0142
Sequence domains: Transcription initiation factor IID, 31kD subunit
Transcription-associated protein Chain: L
Molecule details ›
Chain: L
Length: 3825 amino acids
Theoretical weight: 438.06 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QYV4 (Residues: 1-3825; Coverage: 100%)
Gene name: PAS_chr1-4_0571
Sequence domains:
Transcriptional regulator involved in glucose repression of Gal4p-regulated genes Chain: B
Molecule details ›
Chain: B
Length: 722 amino acids
Theoretical weight: 81.86 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R2A4 (Residues: 1-722; Coverage: 100%)
Gene name: PAS_chr2-2_0284
Sequence domains: Histone acetyltransferases subunit 3
Spt8 Chain: N
Molecule details ›
Chain: N
Length: 400 amino acids
Theoretical weight: 34.06 KDa
Source organism: Komagataella phaffii GS115
Ubiquitin Chain: R
Molecule details ›
Chain: R
Length: 76 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-227; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
Ubiquitin carboxyl-terminal hydrolase Chain: Q
Molecule details ›
Chain: Q
Length: 502 amino acids
Theoretical weight: 56.75 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QY61 (Residues: 1-502; Coverage: 100%)
Gene name: PAS_chr1-4_0341
Sequence domains:
SAGA-associated factor 11 Chain: O
Molecule details ›
Chain: O
Length: 123 amino acids
Theoretical weight: 13.98 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R2D9 (Residues: 1-123; Coverage: 100%)
Gene name: PAS_chr2-2_0251
Sequence domains: Sgf11 (transcriptional regulation protein)
Transcription and mRNA export factor SUS1 Chain: P
Molecule details ›
Chain: P
Length: 96 amino acids
Theoretical weight: 11.13 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R1P1 (Residues: 1-96; Coverage: 100%)
Gene names: PAS_chr2-1_0761, SUS1
Sequence domains: Transcription factor e(y)2

Ligands and Environments

No bound ligands
1 modified residue:
Ligand GLZ 1 x GLZ

Experiments and Validation Details

Entry percentile scores
Resolution: 20Å
Relevant EMDB volumes: EMD-10446
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Structure and mechanism of the RNA polymerase II transcription machinery.
Schier et al. (2020)
13 more

3 mentions without citation

The biochemical and genetic discovery of the SAGA complex.
Grant et al. (2021)
2 more