6EXV Transcription date Nov 09, 2017
title Structure Of Mammalian Rna Polymerase II Elongation Complex By Alpha-Amanitin
authors X.Liu, L.Farnung, C.Wigge, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Ec: 2.7.7.6
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2
Chain: B
Ec: 2.7.7.6

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: D

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: E

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: F

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9,Dna-Directed Rna Poly Subunit I,Rna Polymerase II 14.5 Kda Subunit,Rpb14.5;

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: J
Synonym: Rna Polymerases I,II,And III Subunit Abc5,Dna-Dire Polymerase III Subunit L;

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: K

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: L

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Thymus

Molecule: Amatoxin
Chain: M

Organism_scientific: Amanita Phalloides
Organism_taxid: 67723

Molecule: Dna (25-Mer)
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'-R(Pcpapupapapapgpapcpcpapgpg
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (36-Mer)
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
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 CSX, HYP, ILX, MG, TRX, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


K


L


Primary referenceCryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by alpha-amanitin., Liu X, Farnung L, Wigge C, Cramer P, J Biol Chem. 2018 Mar 17. pii: RA118.002545. doi: 10.1074/jbc.RA118.002545. PMID:29550768
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (604 Kb) [Save to disk]
  • Biological Unit Coordinates (6exv.pdb1.gz) 593 Kb
  • LPC: Ligand-Protein Contacts for 6EXV
  • CSU: Contacts of Structural Units for 6EXV
  • Retrieve 6EXV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6EXV from S2C, [Save to disk]
  • View 6EXV 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 6EXV
  • 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 6exv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6exv_T] [6exv_M] [6exv_D] [6exv_A] [6exv_L] [6exv_J] [6exv_B] [6exv_E] [6exv_K] [6exv_I] [6exv_N] [6exv_F] [6exv_P] [6exv_G] [6exv_C] [6exv_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6EXV
  • Community annotation for 6EXV 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