5M86

Crystal Structure of the Thermoplasma acidophilum Protein Ta1207


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the Thermoplasma acidophilum protein Ta1207.

Pathare, G.R.Nagy, I.Hubert, A.Thomas, D.R.Bracher, A.

(2017) Acta Crystallogr F Struct Biol Commun 73: 328-335

  • DOI: 10.1107/S2053230X17007087
  • Primary Citation of Related Structures:  
    5M86

  • PubMed Abstract: 
  • The crystal structure of the Ta1207 protein from Thermoplasma acidophilum is reported. Ta1207 was identified in a screen for high-molecular-weight protein complexes in T. acidophilum. In solution, Ta1207 forms homopentamers of 188 kDa. The crystal structure of recombinant Ta1207 solved by Se-MAD at 2 ...

    The crystal structure of the Ta1207 protein from Thermoplasma acidophilum is reported. Ta1207 was identified in a screen for high-molecular-weight protein complexes in T. acidophilum. In solution, Ta1207 forms homopentamers of 188 kDa. The crystal structure of recombinant Ta1207 solved by Se-MAD at 2.4 Å resolution revealed a complex with fivefold symmetry. In the crystal lattice, calcium ions induce the formation of a nanocage from two pentamers. The Ta1207 protomers comprise two domains with the same novel α/β topology. A deep pocket with a binding site for a negatively charged group suggests that Ta1207 functions as an intracellular receptor for an unknown ligand. Homologues of Ta1207 occur only in Thermoplasmatales and its function might be related to the extreme lifestyle of these archaea. The thermostable Ta1207 complex might provide a useful fivefold-symmetric scaffold for future nanotechnological applications.


    Organizational Affiliation

    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ta1207
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
333Thermoplasma acidophilum DSM 1728Mutation(s): 0 
Gene Names: Ta1207
UniProt
Find proteins for Q9HIW9 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HIW9 
Go to UniProtKB:  Q9HIW9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth F] , EA [auth G] , HA [auth H] , KA [auth I] , M [auth A] , NA [auth J] , P [auth B] , S [auth C] , 
BA [auth F],  EA [auth G],  HA [auth H],  KA [auth I],  M [auth A],  NA [auth J],  P [auth B],  S [auth C],  V [auth D],  Y [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth G] , FA [auth H] , IA [auth I] , K [auth A] , LA [auth J] , N [auth B] , Q [auth C] , T [auth D] , 
CA [auth G],  FA [auth H],  IA [auth I],  K [auth A],  LA [auth J],  N [auth B],  Q [auth C],  T [auth D],  W [auth E],  Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth F] , DA [auth G] , GA [auth H] , JA [auth I] , L [auth A] , MA [auth J] , O [auth B] , R [auth C] , 
AA [auth F],  DA [auth G],  GA [auth H],  JA [auth I],  L [auth A],  MA [auth J],  O [auth B],  R [auth C],  U [auth D],  X [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A , B , C , D , E , F , G , H , 
A,  B,  C,  D,  E,  F,  G,  H,  I,  J
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.639α = 90
b = 112.821β = 118.7
c = 221.328γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
SHELXDphasing
XDSdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references, Structure summary