6VEN Transferase Structural Protein Dna date Jan 02, 2020
title Yeast Compass In Complex With A Ubiquitinated Nucleosome
authors E.J.Worden, C.Wolberger
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Mutation: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe-81l

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Rosetta 2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Histone H2a Type 1
Chain: C, G
Engineered: Yes
Mutation: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Rosetta 2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: 601 Dna (146-Mer)
Chain: I
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 601 Dna (146-Mer)
Chain: J
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin
Chain: K
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Compass Component Swd3
Chain: L
Synonym: Complex Proteins Associated With Set1 Protein Swd3 Component Swd3;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Swd3, Cps30, Saf35, Ybr175w, Ybr1237
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_strain: Hi Five
Expression_system_vector_type: Bacmid

Molecule: Compass Component Swd1
Chain: M
Synonym: Complex Proteins Associated With Set1 Protein Swd1 Component Swd1;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Swd1, Cps50, Saf49, Yar003w, Fun16
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_strain: Hi Five
Expression_system_vector_type: Bacmid

Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-4 S
Chain: N
Fragment: Unp Residues 762-1080
Synonym: Compass Component Set1,Lysine N-Methyltransferase Domain-Containing Protein 1;
Ec: 2.1.1.354
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Set1, Kmt2, Ytx1, Yhr119w
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_strain: Hi Five
Expression_system_vector_type: Bacmid

Molecule: Compass Component Bre2
Chain: O
Synonym: Brefeldin-A Sensitivity Protein 2,Complex Proteins Associated With Set1 Protein Bre2,Set1c Component Bre2;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Bre2, Cps60, Ylr015w
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_strain: Hi Five
Expression_system_vector_type: Bacmid

Molecule: Compass Component Sdc1
Chain: P, Q
Synonym: Complex Proteins Associated With Set1 Protein Sdc1 Component Sdc1,Suppressor Of Cdc25 Protein 1;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Sdc1, Cps25, Saf19, Ydr469w
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_strain: Hi Five
Expression_system_vector_type: Bacmid

Molecule: Compass Component Spp1
Chain: R
Synonym: Complex Proteins Associated With Set1 Protein Spp1 Component Spp1,Suppressor Of Prp Protein 1;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Spp1, Cps40, Saf41, Ypl138c
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_strain: Hi Five
Expression_system_vector_type: Bacmid
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 3.37 Å
ligand NLE, SAM, ZN enzyme Transferase E.C.2.1.1.354 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


L


M


O


P, Q
  • chromatin silencing at telom...

  • R
  • chromatin silencing at telom...

  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (443 Kb) [Save to disk]
  • Biological Unit Coordinates (6ven.pdb1.gz) 430 Kb
  • LPC: Ligand-Protein Contacts for 6VEN
  • CSU: Contacts of Structural Units for 6VEN
  • Retrieve 6VEN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VEN from S2C, [Save to disk]
  • View 6VEN 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 6VEN
  • 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 6ven from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ven_J] [6ven_G] [6ven_B] [6ven_Q] [6ven_N] [6ven_O] [6ven_K] [6ven_I] [6ven_H] [6ven_C] [6ven_M] [6ven_D] [6ven_F] [6ven_P] [6ven_R] [6ven_A] [6ven_L] [6ven_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6VEN
  • Community annotation for 6VEN at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science