4S20 Transferase Dna Rna date Jan 16, 2015
title Structural Basis For Transcription Reactivation By Rapa
authors B.Liu, Y.Zuo, T.A.Steitz
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, F, G
Synonym: Rnap Subunit Alpha, Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rpoa, Ecdh10b_3470
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, H
Synonym: Rnap Subunit Beta, Rna Polymerase Subunit Beta, Transcriptase Subunit Beta;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rpob, O3k_23925
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, I
Synonym: Rnap Subunit Beta', Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rpoc, O3o_01425
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E, J
Synonym: Rnap Omega Subunit, Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rpoz, O3o_25075
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase-Associated Protein Rapa
Chain: K, L
Synonym: Atp-Dependent Helicase Hepa
Ec: 3.6.4.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rapa, Hepa, Yaba, B0059, Jw0058
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Papcpgpapcptpgpapgpcpcpgpaptp
Chain: M, O
Engineered: Yes
Other_details: Template

Synthetic: Yes

Molecule: 5'-R(Papupcpgpgpcpupcpa)-3'
Chain: N, P
Engineered: Yes
Other_details: Transcript

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.273 R_Free 0.369
crystal
cell
length a length b length c angle alpha angle beta angle gamma
336.090 158.930 255.010 90.00 101.28 90.00
method X-Ray Diffractionresolution 4.70 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene ECDH10B ; O3K ; O3O ; O3O
Gene
Ontology
ChainFunctionProcessComponent
D, I


F, A, B, G


H, C


J, E


K, L


Primary referenceStructural basis for transcription reactivation by RapA., Liu B, Zuo Y, Steitz TA, Proc Natl Acad Sci U S A. 2015 Feb 2. pii: 201417152. PMID:25646438
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2726 Kb) [Save to disk]
  • Biological Unit Coordinates (4s20.pdb1.gz) 1367 Kb
  • Biological Unit Coordinates (4s20.pdb2.gz) 1359 Kb
  • LPC: Ligand-Protein Contacts for 4S20
  • CSU: Contacts of Structural Units for 4S20
  • Structure Factors (1310 Kb)
  • Retrieve 4S20 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4S20 from S2C, [Save to disk]
  • Re-refined 4s20 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4S20 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 4S20
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4S20, from MSDmotif at EBI
  • Fold representative 4s20 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4s20_N] [4s20_J] [4s20_M] [4s20_G] [4s20_F] [4s20_K] [4s20_A] [4s20_L] [4s20_C] [4s20_B] [4s20_P] [4s20_H] [4s20_I] [4s20_O] [4s20_E] [4s20_D] [4s20]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4S20: [DEXDc] [HELICc] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4S20
  • Community annotation for 4S20 at PDBWiki (http://pdbwiki.org)

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