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PDBsum entry 1e0r
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the beta-Apical domain of the thermosome reveals structural plasticity in the protrusion region.
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Authors
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G.Bosch,
W.Baumeister,
L.O.Essen.
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Ref.
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J Mol Biol, 2000,
301,
19-25.
[DOI no: ]
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PubMed id
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Abstract
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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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Figure 2.
Figure 2. Stereo view of the isolated b-apical domain
structure (violet) superimposed on the two crystal forms A and B
of the isolated a-apical domain (yellow and orange) and the
structures of the a and b-apical domains in the intact
thermosome (blue and green). The globular core is shown in grey
for all structures.
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Figure 3.
Figure 3. Influence of the structural context on the
secondary structure of the protrusions. (a) and (b) Interactions
between neighbouring domains in the crystal lattice in the
crystals of the isolated a and b-apical domain. (c) Top view of
the fully closed thermosome showing the circularly closed
b-sheet (generated from PDB entry 1A6D).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
301,
19-25)
copyright 2000.
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Secondary reference #1
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Title
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Crystal structure of the thermosome, The archaeal chaperonin and homolog of cct.
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Authors
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L.Ditzel,
J.Löwe,
D.Stock,
K.O.Stetter,
H.Huber,
R.Huber,
S.Steinbacher.
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Ref.
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Cell, 1998,
93,
125-138.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. General Architecture of Chaperonins(A) Side view
of the hexadecameric thermosome structure.(B) Side view of the
asymmetric GroEL-GroES-(ADP)[7] complex ([77]).Domains are
colored in red (equatorial), green (intermediate), and yellow
(apical). Within each complex domains of aligned subunits are
highlighted in blue (equatorial), light blue (intermediate), and
violet (apical). Bound ADP is drawn in yellow.(C) Top view of
the thermosome α (red/violet) and β (yellow) apical domains.
β strands S12 and S13 and the N-terminal half of helix H10 (lid
segments) form the lid domain that seals off the central
chamber. Helices H10 and H11 and loop L topologically correspond
to helices H and I and the loop connecting β strands 6 and 7 in
GroEL that are involved in substrate and/or GroES binding.Figure
1A Figure 1B Figure 3 Figure 5, and Figure 6A were generated
using BOBSCRIPT ( [18]) and RASTER3D ( [3 and 54]). Figure 1C
was prepared with MOLSCRIPT ( [41]) as modified by D. Peisach
and E. Peisach and with POVRAY.
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Figure 3.
Figure 3. Subunit Structure and Contacts(A) Schematic
drawing of the secondary structural elements of a thermosome α
subunit. Helices and strands are labeled and colored as in
Figure 2. With respect to Figure 1A the view corresponds to a
90° rotation around the pseudo 8-fold axis.(B) Intra-ring
contacts between two thermosome subunits as viewed from the
inside of the particle. The α and β monomers are color coded
as in Figure 1A, and the bound nucleotides are shown in
yellow.(C) Inter-ring contacts between two thermosome α
subunits related by 2-fold symmetry.(D) GroEL inter-ring
contacts. One subunit in the upper ring is related to two
subunits in the lower ring by 2-fold axes at the right and left
edge of the upper subunit.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Structure of the substrate binding domain of the thermosome, An archaeal group ii chaperonin.
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Authors
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M.Klumpp,
W.Baumeister,
L.O.Essen.
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Ref.
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Cell, 1997,
91,
263-270.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. The Helical Protrusion of Group II Apical
Domains(A) Stereo representation of the helical protrusion.
Atoms are colored in yellow (carbon), blue (nitrogen), and red
(oxygen). Residues conserved throughout the group II chaperonins
are labeled (compare Figure 1).(B) Flexibility of the helical
protrusion as shown by the two crystal forms A (yellow) and B
(orange). Residue Tyr301 is shown for illustrating
conformational changes transmitted from the helical protrusions
to the interhelical cleft region.
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Figure 4.
Figure 4. Hydrophobicity of the Surface Regions on Group I
and Group II ChaperoninsSurface representations of the substrate
binding domains of the thermosome α subunit and GroEL were
generated with an increased probe radius of 4 Å using the
program GRASP ([31]). For orientation, C[α]-backbones
(thermosome, yellow; GroEL, green) are shown beneath the
surfaces. The surfaces are color coded according to the
underlying average hydrophobicity found for surface-exposed
residues of group I and group II chaperonins (hydrophobicity
scale as in[37]; red, hydrophobic; blue, hydrophilic). The
interhelical cleft is marked by white arrows.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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