5NSS Transcription date Apr 26, 2017
title Cryo-Em Structure Of Rna Polymerase-Sigma54 Holoenzyme With Dna And Transcription Activator Pspf Intermedate Complex
authors R.Glyde, F.Z.Ye, V.C.Darbari, N.Zhang, M.Buck, X.D.Zhang
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Gene: Rpoa, Pez, Phs, Sez, B3295, Jw3257
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold Plyss Ag
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem

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

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Gene: Rpob, Gron, Nitb, Rif, Ron, Stl, Stv, Tabd, B3987, Jw
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold Plyss Ag
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b+

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

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Gene: Rpoc, Tabb, B3988, Jw3951
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold Plyss Ag

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

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Gene: Rpoz, B3649, Jw3624
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold Plyss Ag
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem

Molecule: Psp Operon Transcriptional Activator
Chain: F, G, J, K, L, N
Synonym: Phage Shock Protein F
Engineered: Yes

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Gene: Pspf, Ycjb, B1303, Jw1296
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold Plyss Ag
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem

Molecule: Non-Template Promoter Dna
Chain: H
Engineered: Yes

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Gene: Rpon
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b+

Molecule: Rna Polymerase Sigma-54 Factor,Rna Polymerase Sig Factor,Rna Polymerase Sigma-54 Factor,Rna Polymerase Sigma- Rna Polymerase Sigma-54 Factor,Rna Polymerase Sigma-54 Fact Polymerase Sigma-54 Factor,Rna Polymerase Sigma-54 Factor,R Polymerase Sigma-54 Factor,Rna Polymerase Sigma-54 Factor,R Polymerase Sigma-54 Factor,Rna Polymerase Sigma-54 Factor,R Polymerase Sigma-54 Factor,Rna Polymerase Sigma-54 Factor,R Polymerase Sigma-54 Factor,Rna Polymerase Sigma-54 Factor,R Polymerase Sigma-54 Factor Rpon,Rna Polymerase Sigma-54 Fac Polymerase Sigma-54 Factor,Rna Polymerase Sigma-54 Factor,R Polymerase Sigma-54 Factor,Rna Polymerase Sigma-54 Factor,R Polymerase Sigma-54 Factor,Rna Polymerase Sigma-54 Factor,R Polymerase Sigma-54 Factor;
Chain: M
Engineered: Yes

Organism_scientific: Klebsiella Pneumoniae
Organism_taxid: 573
Gene: Rpon, Kpst82_0597, Samea3531778_03572, Sm87_03359, Samea4362693_02699, Sm87_03359, Samea4362708_00719;
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold Plyss Ag
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem

Molecule: Template Promoter Dna
Chain: I
Engineered: Yes

Organism_scientific: Klebsiella Pneumoniae
Organism_taxid: 573
Gene: Nifh
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold Plyss Ag
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 5.80 Å
ligand
enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F, J, N, K, G, L


M


Primary referenceStructures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation., Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X, Mol Cell. 2017 Jul 6;67(1):106-116.e4. doi: 10.1016/j.molcel.2017.05.010. Epub, 2017 Jun 1. PMID:28579332
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (676 Kb) [Save to disk]
  • Biological Unit Coordinates (5nss.pdb1.gz) 653 Kb
  • CSU: Contacts of Structural Units for 5NSS
  • Retrieve 5NSS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NSS from S2C, [Save to disk]
  • View 5NSS 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 5NSS
  • 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 5nss from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5nss_N] [5nss_M] [5nss_L] [5nss_C] [5nss_K] [5nss_G] [5nss_J] [5nss_F] [5nss_B] [5nss_D] [5nss_A] [5nss_H] [5nss_E] [5nss_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5NSS
  • Community annotation for 5NSS at PDBWiki (http://pdbwiki.org)

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