4V1M Architecture of the RNA polymerase II-Mediator core transcription initiation complex date
authors Plaschka, C., Lariviere, L., Wenzeck, L., Hemann, M., Tegunov, D., Petrotchenko, E.V., Borchers, C.H., Baumeister, W., Herzog, F., Villa, E., Cramer, P.
compound source
symmetry
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 6.60
ligand BRU, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • RNA-directed 5'-3' RNA polym...


  • B
  • RNA-directed 5'-3' RNA polym...


  • C
  • RNA-directed 5'-3' RNA polym...


  • E
  • RNA-directed 5'-3' RNA polym...


  • F
  • RNA-directed 5'-3' RNA polym...


  • H
  • RNA-directed 5'-3' RNA polym...


  • I
  • RNA-directed 5'-3' RNA polym...


  • J
  • RNA-directed 5'-3' RNA polym...

  • DNA-directed RNA polymerase ...
  • K
  • RNA-directed 5'-3' RNA polym...


  • L
  • RNA-directed 5'-3' RNA polym...


  • Primary referenceArchitecture of the RNA polymerase II-Mediator core initiation complex., Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P, Nature. 2015 Feb 4. doi: 10.1038/nature14229. PMID:25652824
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (610 Kb) [Save to disk]
  • Biological Unit Coordinates (4v1m.pdb1.gz) 600 Kb
  • LPC: Ligand-Protein Contacts for 4V1M
  • CSU: Contacts of Structural Units for 4V1M
  • Retrieve 4V1M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V1M from S2C, [Save to disk]
  • View 4V1M 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 4V1M
  • 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 4V1M, from MSDmotif at EBI
  • Fold representative 4v1m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4v1m_K] [4v1m_F] [4v1m_A] [4v1m_B] [4v1m_N] [4v1m_J] [4v1m_E] [4v1m_I] [4v1m_P] [4v1m_C] [4v1m_H] [4v1m] [4v1m_T] [4v1m_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V1M: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
  • Other resources with information on 4V1M
  • Community annotation for 4V1M at PDBWiki (http://pdbwiki.org)

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