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6t9k

SAGA Core module

Method: ELECTRON MICROSCOPY Dmax: 151.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcription factor SPT20

OrganismNot specified

UniProt P50875

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain B； UniProt 1–604 Not recorded Protein SPT3 × 1 （P06844） Transcription initiation factor TFIID subunit 5 × 1 （P38129） Transcription initiation factor TFIID subunit 6 × 1 （P53040） Transcription initiation factor TFIID subunit 9 × 1 （Q05027） Transcription initiation factor TFIID subunit 10 × 1 （Q12030） Transcriptional coactivator HFI1/ADA1 × 1 （Q12060） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） Transcriptional activator SPT7 × 1 （P35177） SAGA-associated factor 73 × 1 （P53165） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–604（604 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å
6T9J SAGA Tra1 module Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–604（604 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.40 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPT20_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–604； UniProt 1–604

Protein SPT3

OrganismNot specified

UniProt P06844

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain C； UniProt 1–337 Not recorded Transcription factor SPT20 × 1 （P50875） Transcription initiation factor TFIID subunit 5 × 1 （P38129） Transcription initiation factor TFIID subunit 6 × 1 （P53040） Transcription initiation factor TFIID subunit 9 × 1 （Q05027） Transcription initiation factor TFIID subunit 10 × 1 （Q12030） Transcriptional coactivator HFI1/ADA1 × 1 （Q12060） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） Transcriptional activator SPT7 × 1 （P35177） SAGA-associated factor 73 × 1 （P53165） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–337（337 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPT3_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–337； UniProt 1–337

Transcription initiation factor TFIID subunit 5

OrganismNot specified

UniProt P38129

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain D； UniProt 1–798 Not recorded Transcription factor SPT20 × 1 （P50875） Protein SPT3 × 1 （P06844） Transcription initiation factor TFIID subunit 6 × 1 （P53040） Transcription initiation factor TFIID subunit 9 × 1 （Q05027） Transcription initiation factor TFIID subunit 10 × 1 （Q12030） Transcriptional coactivator HFI1/ADA1 × 1 （Q12060） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） Transcriptional activator SPT7 × 1 （P35177） SAGA-associated factor 73 × 1 （P53165） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2J49 Crystal structure of yeast TAF5 N-terminal domain Deposited 2006-08-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 147–290（144 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 147-290
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.05 M CACODYLATE PH 6.5,2.4 M NA FORMATE
Resolution 2.30 Å R-free 0.270
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–798（798 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TAF5_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–798； UniProt 1–798

Transcription initiation factor TFIID subunit 6

OrganismNot specified

UniProt P53040

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain E； UniProt 1–516 Not recorded Transcription factor SPT20 × 1 （P50875） Protein SPT3 × 1 （P06844） Transcription initiation factor TFIID subunit 5 × 1 （P38129） Transcription initiation factor TFIID subunit 9 × 1 （Q05027） Transcription initiation factor TFIID subunit 10 × 1 （Q12030） Transcriptional coactivator HFI1/ADA1 × 1 （Q12060） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） Transcriptional activator SPT7 × 1 （P35177） SAGA-associated factor 73 × 1 （P53165） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–516（516 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TAF6_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–516； UniProt 1–516

Transcription initiation factor TFIID subunit 9

OrganismNot specified

UniProt Q05027

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain F； UniProt 1–157 Not recorded Transcription factor SPT20 × 1 （P50875） Protein SPT3 × 1 （P06844） Transcription initiation factor TFIID subunit 5 × 1 （P38129） Transcription initiation factor TFIID subunit 6 × 1 （P53040） Transcription initiation factor TFIID subunit 10 × 1 （Q12030） Transcriptional coactivator HFI1/ADA1 × 1 （Q12060） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） Transcriptional activator SPT7 × 1 （P35177） SAGA-associated factor 73 × 1 （P53165） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–157（157 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TAF9_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 1–157； UniProt 1–157

Transcription initiation factor TFIID subunit 10

OrganismNot specified

UniProt Q12030

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain G； UniProt 1–206 Not recorded Transcription factor SPT20 × 1 （P50875） Protein SPT3 × 1 （P06844） Transcription initiation factor TFIID subunit 5 × 1 （P38129） Transcription initiation factor TFIID subunit 6 × 1 （P53040） Transcription initiation factor TFIID subunit 9 × 1 （Q05027） Transcriptional coactivator HFI1/ADA1 × 1 （Q12060） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） Transcriptional activator SPT7 × 1 （P35177） SAGA-associated factor 73 × 1 （P53165） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–206（206 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TAF10_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain G； PDBConstruct 1–206； UniProt 1–206

Transcriptional coactivator HFI1/ADA1

OrganismNot specified

UniProt Q12060

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain H； UniProt 1–488 Not recorded Transcription factor SPT20 × 1 （P50875） Protein SPT3 × 1 （P06844） Transcription initiation factor TFIID subunit 5 × 1 （P38129） Transcription initiation factor TFIID subunit 6 × 1 （P53040） Transcription initiation factor TFIID subunit 9 × 1 （Q05027） Transcription initiation factor TFIID subunit 10 × 1 （Q12030） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） Transcriptional activator SPT7 × 1 （P35177） SAGA-associated factor 73 × 1 （P53165） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–488（488 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HFI1_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain H； PDBConstruct 1–488； UniProt 1–488

Transcription initiation factor TFIID subunit 12

OrganismNot specified

UniProt Q03761

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain I； UniProt 1–539 Not recorded Transcription factor SPT20 × 1 （P50875） Protein SPT3 × 1 （P06844） Transcription initiation factor TFIID subunit 5 × 1 （P38129） Transcription initiation factor TFIID subunit 6 × 1 （P53040） Transcription initiation factor TFIID subunit 9 × 1 （Q05027） Transcription initiation factor TFIID subunit 10 × 1 （Q12030） Transcriptional coactivator HFI1/ADA1 × 1 （Q12060） Transcriptional activator SPT7 × 1 （P35177） SAGA-associated factor 73 × 1 （P53165） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 1–539（539 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å
6T9J SAGA Tra1 module Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–539（539 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.40 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TAF12_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain I； PDBConstruct 1–539； UniProt 1–539

Transcriptional activator SPT7

OrganismNot specified

UniProt P35177

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain K； UniProt 1–1332 Not recorded Transcription factor SPT20 × 1 （P50875） Protein SPT3 × 1 （P06844） Transcription initiation factor TFIID subunit 5 × 1 （P38129） Transcription initiation factor TFIID subunit 6 × 1 （P53040） Transcription initiation factor TFIID subunit 9 × 1 （Q05027） Transcription initiation factor TFIID subunit 10 × 1 （Q12030） Transcriptional coactivator HFI1/ADA1 × 1 （Q12060） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） SAGA-associated factor 73 × 1 （P53165） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain K 1–1332（1332 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPT7_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain K； PDBConstruct 1–1332； UniProt 1–1332

SAGA-associated factor 73

OrganismNot specified

UniProt P53165

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain Q； UniProt 1–657 Not recorded Transcription factor SPT20 × 1 （P50875） Protein SPT3 × 1 （P06844） Transcription initiation factor TFIID subunit 5 × 1 （P38129） Transcription initiation factor TFIID subunit 6 × 1 （P53040） Transcription initiation factor TFIID subunit 9 × 1 （Q05027） Transcription initiation factor TFIID subunit 10 × 1 （Q12030） Transcriptional coactivator HFI1/ADA1 × 1 （Q12060） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） Transcriptional activator SPT7 × 1 （P35177） unassigned sequence × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions：Cryogen ETHANE；blot for 4 seconds before plunging Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LO3 Solution structure of Sgf73(59-102) zinc finger domain Deposited 2012-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 59–102（44 aa） Fragment：UNP residues 59-102
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.175；Pressure ambient
NMR sample composition 0.2 mM [U-98% 15N] sgf73, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 mM TCEP, 10 % D2O, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-99% 13C; U-98% 15N] sgf73, 20 mM sodium phosphate, 75 mM sodium chloride, 1 mM DTT, 10 % D2O, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.2 mM [U-98% 15N] sgf73, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 mM TCEP, 100 % D2O, 100% D2O | 100% D2O
Resolution not provided
3M99 Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module Deposited 2010-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–104（104 aa） Fragment：UNP RESIDUES: 1-104
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.2M ammonium citrate, 18% PEG 3,350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.300
3MHH Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module Deposited 2010-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–96（96 aa） Fragment：residues 1-96
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1 M Na Citrate (5.2), 16% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.45 Å R-free 0.273
3MHS Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde Deposited 2010-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–96（96 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.89 Å R-free 0.208
4FIP Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–96（96 aa） Fragment：UNP Residues 1-96
Chain H 1–96（96 aa） Fragment：UNP Residues 1-96
Not recorded ZN ZINC ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M Tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.69 Å R-free 0.264
4FJC Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–96（96 aa） Fragment：UNP Residues 1-96
Chain H 1–96（96 aa） Fragment：UNP Residues 1-96
Not recorded ZN ZINC ION × 14 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.83 Å R-free 0.276
4FK5 Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module Deposited 2012-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–96（96 aa） Fragment：UNP Residues 1-96
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；sodium citrate pH 5.2, 16% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.03 Å R-free 0.212
4W4U Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution Deposited 2014-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–96（96 aa）
Mutation：Y57A ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris,18% PEG3350, 100mM Ammonium Sulfate
Resolution 2.80 Å R-free 0.241
4W4U Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution Deposited 2014-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 1–96（96 aa）
Mutation：Y57A ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris,18% PEG3350, 100mM Ammonium Sulfate
Resolution 2.80 Å R-free 0.241
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–96（96 aa）
Mutation：N59D ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate
Resolution 2.36 Å R-free 0.244
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 1–96（96 aa）
Mutation：N59D ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate
Resolution 2.36 Å R-free 0.244
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–96（96 aa）
Chain H 1–96（96 aa）
Mutation：N59D Mutation：N59D ZN ZINC ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate
Resolution 2.36 Å R-free 0.244
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain Y 1–104（104 aa）
Chain d 1–104（104 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain i 1–104（104 aa）
Chain n 1–104（104 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
6AQR SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin Deposited 2017-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–96（96 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES pH 7.0 17% PEG3350 0.1 M ammonium sulfate
Resolution 2.10 Å R-free 0.249
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain Q 1–657（657 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–657（657 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.60 Å

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SGF73_YEAST
Isoform —
PDB entities 10
Chains and sequence ranges Author chain Q； PDBConstruct 1–657； UniProt 1–657

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6t9k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6t9k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6t9k
Deposition date deposition_date2019-10-28
Structure title titleSAGA Core module
Keywords keywordsCoactivator, Transcription, Histone acetyltransferase, Histone deubiquitinase, GENE REGULATION; GENE REGULATION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier45.21 Å
Radius of gyration Rg (electron density) rg_electron45.03 Å
Forward intensity I(0) i01081530000.00
Molecular weight molecular_weight273110.0 kDa
Excluded volume excluded_volume342510 ų
Envelope volume envelope_volume476600 ų
Hydration-shell volume shell_volume86034 ų
Envelope diameter envelope_diameter161.4 Å
Shell Rg shell_rg50.87 Å
Envelope Rg envelope_rg45.46 Å
Shape Rg shape_rg45.03 Å
Total Rg total_rg45.31 Å
Total atoms total_atoms19241
Residues n_residues2425
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax151.2 Å
Rg (real space) rg_real45.25 Å
Rg uncertainty (real space) rg_real_error1.51 Å
I(0) (real space) i0_real1.0820e+09
I(0) uncertainty (real space) i0_real_error2.1410e+07
Rg (reciprocal space) rg_reciprocal45.21 Å
I(0) (reciprocal space) i0_reciprocal1081000000.0000
Solution quality estimate total_estimate0.8654
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.9 Å
Skewness Skewness skewness0.414
Kurtosis Kurtosis kurtosis-0.283
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha229400000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.793
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

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8. Citations (1)

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9. Files and Curves (10)