1SMY Transferase date Mar 10, 2004
title Structural Basis For Transcription Regulation By Alarmone Ppgpp
authors I.Artsimovitch, V.Patlan, S.Sekine, M.N.Vassylyeva, T.Hosaka, K.Ochi, S.Yokoyama, D.G.Vassylyev, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Dna-Directed Rna Polymerase Alpha Chain
Chain: A, B, K, L
Synonym: Rnap Alpha Subunit, Transcriptase Alpha Chain, Rna Polymerase Alpha Subunit;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

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

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Rna Polymerase Omega Subunit
Chain: E, O

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Principal Sigma Factor
Chain: F, P

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 32
R_factor 0.186 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
236.350 236.350 249.040 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand G4P, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
related structures by homologous chain: 1IW7, 1KU2
Gene
Ontology
ChainFunctionProcessComponent
A, K, B, L


F, P


M, C


N, D


O, E


Primary referenceStructural basis for transcription regulation by alarmone ppGpp., Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG, Cell 2004 Apr 30;117(3):299-310. PMID:15109491
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1327 Kb) [Save to disk]
  • Biological Unit Coordinates (1smy.pdb1.gz) 655 Kb
  • Biological Unit Coordinates (1smy.pdb2.gz) 656 Kb
  • LPC: Ligand-Protein Contacts for 1SMY
  • CSU: Contacts of Structural Units for 1SMY
  • Likely Quarternary Molecular Structure file(s) for 1SMY
  • Structure Factors (3199 Kb)
  • Retrieve 1SMY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SMY from S2C, [Save to disk]
  • Re-refined 1smy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SMY 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 1SMY
  • 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
  • 3D motif for 1SMY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1smya1, region A:1-49,A:173-229 [Jmol] [rasmolscript] [script source]
        - Domain d1smya2, region A:50-172 [Jmol] [rasmolscript] [script source]
        - Domain d1smyb1, region B:1-49,B:173-229 [Jmol] [rasmolscript] [script source]
        - Domain d1smyb2, region B:50-172 [Jmol] [rasmolscript] [script source]
        - Domain d1smyc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1smyd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1smye_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1smyf1, region F:258-318 [Jmol] [rasmolscript] [script source]
        - Domain d1smyf2, region F:319-423 [Jmol] [rasmolscript] [script source]
        - Domain d1smyf3, region F:74-257 [Jmol] [rasmolscript] [script source]
        - Domain d1smyk1, region K:1-49,K:173-229 [Jmol] [rasmolscript] [script source]
        - Domain d1smyk2, region K:50-172 [Jmol] [rasmolscript] [script source]
        - Domain d1smyl1, region L:1-49,L:173-229 [Jmol] [rasmolscript] [script source]
        - Domain d1smyl2, region L:50-172 [Jmol] [rasmolscript] [script source]
        - Domain d1smym_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1smyn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1smyo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1smyp1, region P:258-318 [Jmol] [rasmolscript] [script source]
        - Domain d1smyp2, region P:319-423 [Jmol] [rasmolscript] [script source]
        - Domain d1smyp3, region P:74-257 [Jmol] [rasmolscript] [script source]
  • Fold representative 1smy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1smy_N] [1smy_L] [1smy_D] [1smy_B] [1smy_P] [1smy_A] [1smy_F] [1smy_M] [1smy_O] [1smy_K] [1smy] [1smy_C] [1smy_E]
  • SWISS-PROT database: [Q9WX78] [Q9Z9H6] [Q8RQE9] [Q8RQE8] [Q8RQE7]
  • Domain organization of [Q9WX78_THETH] [RPOA_THETH] [RPOB_THET8] [RPOC_THET8] [RPOZ_THET8] by SWISSPFAM
  • Domains found in 1SMY: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 1SMY
  • Community annotation for 1SMY at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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