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- PDB-4xcd: Crystal structure of an octadecameric TF55 complex from S. solfat... -

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Basic information

Entry
Database: PDB / ID: 4xcd
TitleCrystal structure of an octadecameric TF55 complex from S. solfataricus
ComponentsThermosome subunit beta
KeywordsCHAPERONE / Protein Folding / Thermosomes / Chaperonin
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / Thermosome, archaeal / GroEL / GroEL / : / Chaperonins TCP-1 signature 1. / : ...GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / Thermosome, archaeal / GroEL / GroEL / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Thermosome subunit beta
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 Å
AuthorsChaston, J.J. / Stewart, A.G. / Smits, C. / Stock, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP1093649 Australia
CitationJournal: Structure / Year: 2016
Title: Structural and Functional Insights into the Evolution and Stress Adaptation of Type II Chaperonins.
Authors: Jessica J Chaston / Callum Smits / David Aragão / Andrew S W Wong / Bilal Ahsan / Sara Sandin / Sudheer K Molugu / Sanjay K Molugu / Ricardo A Bernal / Daniela Stock / Alastair G Stewart /
Abstract: Chaperonins are essential biological complexes assisting protein folding in all kingdoms of life. Whereas homooligomeric bacterial GroEL binds hydrophobic substrates non-specifically, the ...Chaperonins are essential biological complexes assisting protein folding in all kingdoms of life. Whereas homooligomeric bacterial GroEL binds hydrophobic substrates non-specifically, the heterooligomeric eukaryotic CCT binds specifically to distinct classes of substrates. Sulfolobales, which survive in a wide range of temperatures, have evolved three different chaperonin subunits (α, β, γ) that form three distinct complexes tailored for different substrate classes at cold, normal, and elevated temperatures. The larger octadecameric β complexes cater for substrates under heat stress, whereas smaller hexadecameric αβ complexes prevail under normal conditions. The cold-shock complex contains all three subunits, consistent with greater substrate specificity. Structural analysis using crystallography and electron microscopy reveals the geometry of these complexes and shows a novel arrangement of the α and β subunits in the hexadecamer enabling incorporation of the γ subunit.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermosome subunit beta
B: Thermosome subunit beta
C: Thermosome subunit beta
D: Thermosome subunit beta
E: Thermosome subunit beta
F: Thermosome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,78612
Polymers370,2236
Non-polymers2,5636
Water00
1
A: Thermosome subunit beta
B: Thermosome subunit beta
C: Thermosome subunit beta
D: Thermosome subunit beta
E: Thermosome subunit beta
F: Thermosome subunit beta
hetero molecules

A: Thermosome subunit beta
B: Thermosome subunit beta
C: Thermosome subunit beta
D: Thermosome subunit beta
E: Thermosome subunit beta
F: Thermosome subunit beta
hetero molecules

A: Thermosome subunit beta
B: Thermosome subunit beta
C: Thermosome subunit beta
D: Thermosome subunit beta
E: Thermosome subunit beta
F: Thermosome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,118,35936
Polymers1,110,66918
Non-polymers7,69018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area56300 Å2
ΔGint-339 kcal/mol
Surface area407570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.360, 163.360, 327.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
SymmetryPoint symmetry: (Schoenflies symbol: C9 (9 fold cyclic))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA30 - 53443 - 547
21ALAALABB30 - 53443 - 547
12LYSLYSAA30 - 53643 - 549
22LYSLYSCC30 - 53643 - 549
13ALAALAAA30 - 53443 - 547
23ALAALADD30 - 53443 - 547
14LYSLYSAA30 - 53643 - 549
24LYSLYSEE30 - 53643 - 549
15GLYGLYAA30 - 53543 - 548
25GLYGLYFF30 - 53543 - 548
16GLYGLYBB30 - 53543 - 548
26GLYGLYCC30 - 53543 - 548
17ALAALABB30 - 53443 - 547
27ALAALADD30 - 53443 - 547
18GLYGLYBB30 - 53543 - 548
28GLYGLYEE30 - 53543 - 548
19GLYGLYBB30 - 53543 - 548
29GLYGLYFF30 - 53543 - 548
110ALAALACC30 - 53443 - 547
210ALAALADD30 - 53443 - 547
111LYSLYSCC30 - 53643 - 549
211LYSLYSEE30 - 53643 - 549
112GLYGLYCC30 - 53543 - 548
212GLYGLYFF30 - 53543 - 548
113ALAALADD30 - 53443 - 547
213ALAALAEE30 - 53443 - 547
114ALAALADD30 - 53443 - 547
214ALAALAFF30 - 53443 - 547
115GLYGLYEE30 - 53543 - 548
215GLYGLYFF30 - 53543 - 548

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Thermosome subunit beta / Chaperonin subunit beta / Thermophilic factor 55 beta / TF55-beta / Thermosome subunit 2


Mass: 61703.859 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: thsB, SSO0282 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2T8
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES-Na, sodium formate, TMAO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11K, H, -L20.499
ReflectionResolution: 3.78→65.38 Å / Num. obs: 48892 / % possible obs: 99.4 % / Redundancy: 6.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.142 / Net I/σ(I): 5.2 / Num. measured all: 312308 / Scaling rejects: 57
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.78-3.916.12.2550.92536141860.3780.99293.6
15.14-65.386.20.0353149017890.9970.01698.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Aimless0.3.6data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ko1

3ko1


Resolution: 3.79→64.93 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.885 / SU B: 23.808 / SU ML: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 3645 10.5 %RANDOM
Rwork0.2396 31143 --
obs0.2438 -71.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 485.46 Å2 / Biso mean: 176.892 Å2 / Biso min: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1--28.33 Å20 Å20 Å2
2---28.33 Å20 Å2
3---56.66 Å2
Refinement stepCycle: final / Resolution: 3.79→64.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22955 0 162 0 23117
Biso mean--158.17 --
Num. residues----3016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01923348
X-RAY DIFFRACTIONr_bond_other_d0.0050.0224028
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.98731526
X-RAY DIFFRACTIONr_angle_other_deg1.075354949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.48152997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96625.714945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.968154464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.88715130
X-RAY DIFFRACTIONr_chiral_restr0.050.23767
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0226296
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024498
X-RAY DIFFRACTIONr_mcbond_it7.5817.59212045
X-RAY DIFFRACTIONr_mcbond_other7.5817.59212044
X-RAY DIFFRACTIONr_mcangle_it13.07926.36215023
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A317260.05
12B317260.05
21A303140.11
22C303140.11
31A314720.06
32D314720.06
41A299830.11
42E299830.11
51A316720.05
52F316720.05
61B304570.1
62C304570.1
71B314640.05
72D314640.05
81B301740.11
82E301740.11
91B319540.04
92F319540.04
101C306060.11
102D306060.11
111C313400.07
112E313400.07
121C305520.1
122F305520.1
131D300470.11
132E300470.11
141D315740.05
142F315740.05
151E303090.11
152F303090.11
LS refinement shellResolution: 3.794→3.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 79 -
Rwork0.335 568 -
all-647 -
obs--17.85 %

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