6T9L Gene Regulation date Oct 28, 2019
title Saga Dub Module Bound To A Ubiqitinated Nucleosome
authors H.Wang, P.Cramer
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a
Chain: C, G
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b 1.1
Chain: D
Synonym: H2b1.1
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b
Chain: H
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: Western Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Widom601 Dna (145-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Widom601 Dna (145-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 8
Chain: K
Synonym: Deubiquitinating Enzyme 8,Ubiquitin Thioesterase 8 Ubiquitin-Specific-Processing Protease 8;
Ec: 3.4.19.12
Engineered: Yes
Other_details: This Is A Zinc Containing Protein.

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Ubp8, Ymr223w, Ym9959.05
Expression_system: Saccharomyces Cerevisiae S288c
Expression_system_taxid: 559292

Molecule: Transcription And Mrna Export Factor Sus1
Chain: L

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Saga-Associated Factor 11
Chain: M
Synonym: 11 Kda Saga-Associated Factor
Other_details: This A Zinc-Finger Containing Protein.

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Saga-Associated Factor 73
Chain: N
Synonym: 73 Kda Saga-Associated Factor,Saga Histone Acetylt Complex 73 Kda Subunit;
Other_details: This A Zinc-Finger Containing Protein.

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Polyubiquitin-C
Chain: O
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.60 Å
ligand ZN enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


K


L
  • enzyme activator activity


  • M
  • enzyme activator activity


  • N
  • enzyme activator activity


  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (328 Kb) [Save to disk]
  • Biological Unit Coordinates (6t9l.pdb1.gz) 319 Kb
  • LPC: Ligand-Protein Contacts for 6T9L
  • CSU: Contacts of Structural Units for 6T9L
  • Retrieve 6T9L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6T9L from S2C, [Save to disk]
  • View 6T9L in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6T9L
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6t9l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6t9l_J] [6t9l_A] [6t9l_F] [6t9l_E] [6t9l_D] [6t9l_B] [6t9l_G] [6t9l_C] [6t9l_K] [6t9l_O] [6t9l_I] [6t9l_H] [6t9l_M] [6t9l_L] [6t9l_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6T9L
  • Community annotation for 6T9L at PDBWiki (http://pdbwiki.org)

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