4JKR Transcription, Transferase date Mar 11, 2013
title Crystal Structure Of E. Coli Rna Polymerase In Complex With
authors Y.Zuo, Y.Wang, T.A.Steitz
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, G, H
Synonym: Rnap Subunit Alpha, Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 1133853
Strain: K12 Dh10b
Gene: Ecdh10b_3470, O3o_23125, Rpoa
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, 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: 536056
Strain: 2011c-3493
Gene: Ecdh1me8569_3846, Ecdh1_4008, O3k_23925, Rpob
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Escherichia Coli
Organism_taxid: 595496
Strain: 2009el-2071
Gene: Bwg_3647, O3o_01425, Rpoc
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Escherichia Coli
Organism_taxid: 536056
Strain: 2009el-2071
Gene: Ecdh1me8569_3534, Ecdh1_0056, O3o_25075, Rpoz
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase Sigma Factor Rpod
Chain: F, L
Synonym: Sigma-70
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: Alt, B3067, Jw3039, Rpod
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.247 R_Free 0.318
crystal
cell
length a length b length c angle alpha angle beta angle gamma
187.575 206.164 311.062 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.20 Å
ligand G4P, SR, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene BWG ; ECDH10B ; ECDH1ME8569 ; ECDH1ME8569 ; ECDH1 ; ECDH1 ; O3K ; O3O ; O3O ; O3O
Gene
Ontology
ChainFunctionProcessComponent
A, B, H, G


C, I


F, L


J, D


K, E


Primary referenceThe Mechanism of E. coli RNA Polymerase Regulation by ppGpp Is Suggested by the Structure of their Complex., Zuo Y, Wang Y, Steitz TA, Mol Cell. 2013 May 9;50(3):430-6. doi: 10.1016/j.molcel.2013.03.020. Epub 2013, Apr 25. PMID:23623685
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2613 Kb) [Save to disk]
  • Biological Unit Coordinates (4jkr.pdb1.gz) 1306 Kb
  • Biological Unit Coordinates (4jkr.pdb2.gz) 1309 Kb
  • LPC: Ligand-Protein Contacts for 4JKR
  • CSU: Contacts of Structural Units for 4JKR
  • Structure Factors (1327 Kb)
  • Retrieve 4JKR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JKR from S2C, [Save to disk]
  • Re-refined 4jkr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JKR 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 4JKR
  • 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 4JKR, from MSDmotif at EBI
  • Fold representative 4jkr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jkr_L] [4jkr] [4jkr_E] [4jkr_B] [4jkr_J] [4jkr_G] [4jkr_I] [4jkr_F] [4jkr_K] [4jkr_A] [4jkr_H] [4jkr_C] [4jkr_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4JKR: [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4JKR
  • Community annotation for 4JKR at PDBWiki (http://pdbwiki.org)

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