5VI8 Transcription date Apr 14, 2017
title Structure Of A Mycobacterium Smegmatis Transcription Initiat Complex With An Upstream-Fork Promoter Fragment
authors E.A.Hubin, E.A.Campbell, S.A.Darst
compound source
Molecule: Rna Polymerase-Binding Protein Rbpa
Chain: J
Engineered: Yes
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Rbpa, Msmeg_3858, Msmei_3768
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

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

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

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

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Engineered: Yes

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Rpod, Siga, Msmeg_2758, Msmei_2690
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693

Molecule: Dna (31-Mer)
Chain: O
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (26-Mer)
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: T
Fragment: C-Terminal Residues 251-350
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
symmetry Space Group: P 1 21 1
R_factor 0.240 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
133.012 161.633 139.211 90.00 107.72 90.00
method X-Ray Diffractionresolution 2.76 Å
ligand EDO, MG, SO4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene MSMEG ; MSMEG ; MSMEI ; MSMEI
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F


J


T


Primary referenceStructure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA., Hubin EA, Fay A, Xu C, Bean JM, Saecker RM, Glickman MS, Darst SA, Campbell EA, Elife. 2017 Jan 9;6. pii: e22520. doi: 10.7554/eLife.22520. PMID:28067618
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (557 Kb) [Save to disk]
  • Biological Unit Coordinates (5vi8.pdb1.gz) 544 Kb
  • LPC: Ligand-Protein Contacts for 5VI8
  • CSU: Contacts of Structural Units for 5VI8
  • Structure Factors (3042 Kb)
  • Retrieve 5VI8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VI8 from S2C, [Save to disk]
  • Re-refined 5vi8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VI8 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 5VI8
  • 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 5vi8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vi8_D] [5vi8_C] [5vi8_P] [5vi8_J] [5vi8_T] [5vi8_O] [5vi8_E] [5vi8_A] [5vi8_B] [5vi8_F] [5vi8]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VI8
  • Community annotation for 5VI8 at PDBWiki (http://pdbwiki.org)

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