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.

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

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

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48424
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48425
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B]
AF3 Query on AF3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B]

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

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Entry History

Deposition Data

Released Date: 1999-03-23

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations, Other