1E0R | pdb_00001e0r

Beta-apical domain of thermosome

• PDB DOI: https://doi.org/10.2210/pdb1E0R/pdb

• Classification: CHAPERONIN
• Organism(s): Thermoplasma acidophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2000-04-06 Released: 2000-08-19 
• Deposition Author(s): Bosch, G., Baumeister, W., Essen, L.-O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.318 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Beta-Apical Domain from Thermosome Reveals Structural Plasticity in Protrusion Region

Bosch, G., Baumeister, W., Essen, L.-O.

(2000) J Mol Biology 301: 19

• PubMed: 10926489 
• DOI: https://doi.org/10.1006/jmbi.2000.3955
• Primary Citation Related Structures: 
  1E0R


• PubMed Abstract: 
  

  The crystal structure of the beta-apical domain of the thermosome, an archaeal group II chaperonin from Thermoplasma acidophilum, has been determined at 2.8 A resolution. The structure shows an invariant globular core from which a 25 A long protrusion emanates, composed of an elongated alpha-helix (H10) and a long extended stretch consisting of residues GluB245-ThrB253. A comparison with previous apical domain structures reveals a large segmental displacement of the protruding part of helix H10 via the hinge GluB276-ValB278. The region comprising residues GluB245-ThrB253 adopts an extended beta-like conformation rather than the alpha-helix seen in the alpha-apical domain. Consequently, it appears that the protrusions of the apical domains from group II chaperonins might assume a variety of context-dependent conformations during an open, substrate-accepting state of the chaperonin. Sequence variations in the protrusion regions that are found in the eukaryotic TRiC/CCT subunits may provide different structural propensities and hence serve different roles in substrate recognition.

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Organizational Affiliation: 
• Max-Planck-Institute for Biochemistry, Am Klopferspitz 18a, Martinsried bei München, D-82152, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 17.76 kDa 
• Atom Count: 1,160 
• Modeled Residue Count: 154 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THERMOSOME	A [auth B]	159	Thermoplasma acidophilum	Mutation(s): 3  EC: 5.6.1.7
UniProt
Find proteins for P48425 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore P48425  Go to UniProtKB:  P48425

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.318 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.32	α = 90
b = 57.32	β = 90
c = 106.14	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-19 
Deposition Author(s): Bosch, G., Baumeister, W., Essen, L.-O.

Revision History  

• Version 1.0: 2000-08-19
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2023-12-06
  Changes: Data collection, Database references, Other, Refinement description