1A6E

THERMOSOME-MG-ADP-ALF3 COMPLEX

• PDB DOI:  https://doi.org/10.2210/pdb1A6E/pdb

• Classification: CHAPERONIN
• Organism(s): Thermoplasma acidophilum
• Mutation(s): No 


• Deposited: 1998-02-24 Released: 1999-03-23 
• Deposition Author(s): Ditzel, L., Loewe, J., Stock, D., Stetter, K.-O., Huber, H., Huber, R., Steinbacher, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.285 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Literature

Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT.

Ditzel, L., Lowe, J., Stock, D., Stetter, K.O., Huber, H., Huber, R., Steinbacher, S.

(1998) Cell 93: 125-138

• PubMed: 9546398 
• DOI: https://doi.org/10.1016/s0092-8674(00)81152-6
• Primary Citation of Related Structures:  
  1A6D, 1A6E


• PubMed Abstract: 
  

We have determined to 2.6 A resolution the crystal structure of the thermosome, the archaeal group II chaperonin from T. acidophilum. The hexadecameric homolog of the eukaryotic chaperonin CCT/TRiC shows an (alphabeta)4(alphabeta)4 subunit assembly. Domain folds are homologous to GroEL but form a novel type of inter-ring contact. The domain arrangement resembles the GroEL-GroES cis-ring. Parts of the apical domains form a lid creating a closed conformation. The lid substitutes for a GroES-like cochaperonin that is absent in the CCT/TRiC system. The central cavity has a polar surface implicated in protein folding. Binding of the transition state analog Mg-ADP-AIF3 suggests that the closed conformation corresponds to the ATP form.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Hetero 16-mer - A8B8 Pseudo Symmetry: Dihedral - D8  (3D View)
Pseudo Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Cyclic - C8  (3D View)
Pseudo Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.95 kDa 
• Atom Count: 7,648 
• Modelled Residue Count: 1,005 
• Deposited Residue Count: 1,088 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THERMOSOME (ALPHA SUBUNIT)	A	545	Thermoplasma acidophilum	Mutation(s): 0
UniProt
Find proteins for P48424 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore P48424  Go to UniProtKB:  P48424

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THERMOSOME (BETA SUBUNIT)	B	543	Thermoplasma acidophilum	Mutation(s): 0
UniProt
Find proteins for P48425 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore P48425  Go to UniProtKB:  P48425

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AF3	E [auth A], H [auth B]	ALUMINUM FLUORIDE Al F3 KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.285 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.8	α = 90
b = 167.8	β = 90
c = 202.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-23 
Deposition Author(s): Ditzel, L., Loewe, J., Stock, D., Stetter, K.-O., Huber, H., Huber, R., Steinbacher, S.

Revision History  

• Version 1.0: 1999-03-23
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance