4YLP Transcription Dna Rna date Mar 05, 2015
title E. Coli Transcription Initiation Complex - 16-Bp Spacer And
authors Y.Zuo, T.A.Steitz
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, G, H, M, N
Fragment: N-Terminal Domain (Unp Residues 1-235)
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, Ece24377a_3778
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, I, O
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, Ece24377a_4528
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, J, P
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, Ece24377a_4529
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E, K, Q
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, Ece24377a_4152
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

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

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rpod, Alt, B3067, Jw3039
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Nt Strand Dna (49-Mer)
Chain: 1, 4, 7
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: T Strand Dna (49-Mer)
Chain: 2, 5, 8
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'-R((Gtp))-R(Papgpupc)-3')
Chain: 3, 6, 9
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.231 R_Free 0.313
crystal
cell
length a length b length c angle alpha angle beta angle gamma
237.674 204.988 248.838 90.00 116.86 90.00
method X-Ray Diffractionresolution 5.50 Å
ligand GTP, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene ECE24377A ; ECE24377A ; ECE24377A ; ECE24377A
Gene
Ontology
ChainFunctionProcessComponent
C, O, I


F, L, R


J, P, D


K, E, Q


N, M, A, B, H, G


Primary referenceCrystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble., Zuo Y, Steitz TA, Mol Cell. 2015 Apr 8. pii: S1097-2765(15)00175-6. doi:, 10.1016/j.molcel.2015.03.010. PMID:25866247
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (4158 Kb) [Save to disk]
  • Biological Unit Coordinates (4ylp.pdb1.gz) 1397 Kb
  • Biological Unit Coordinates (4ylp.pdb2.gz) 1400 Kb
  • Biological Unit Coordinates (4ylp.pdb3.gz) 1391 Kb
  • LPC: Ligand-Protein Contacts for 4YLP
  • CSU: Contacts of Structural Units for 4YLP
  • Structure Factors (1299 Kb)
  • Retrieve 4YLP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YLP from S2C, [Save to disk]
  • Re-refined 4ylp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YLP 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 4YLP
  • 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 4YLP, from MSDmotif at EBI
  • Fold representative 4ylp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ylp_L] [4ylp_C] [4ylp_O] [4ylp_D] [4ylp_B] [4ylp_3] [4ylp] [4ylp_N] [4ylp_H] [4ylp_6] [4ylp_8] [4ylp_F] [4ylp_G] [4ylp_R] [4ylp_Q] [4ylp_P] [4ylp_I] [4ylp_1] [4ylp_9] [4ylp_E] [4ylp_4] [4ylp_5] [4ylp_2] [4ylp_J] [4ylp_M] [4ylp_A] [4ylp_K] [4ylp_7]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YLP: [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4YLP
  • Community annotation for 4YLP at PDBWiki (http://pdbwiki.org)

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