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- PDB-4xcg: Crystal structure of a hexadecameric TF55 complex from S. solfata... -

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Basic information

Entry
Database: PDB / ID: 4xcg
TitleCrystal structure of a hexadecameric TF55 complex from S. solfataricus, crystal form I
Components
  • Thermosome subunit alpha
  • Thermosome 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 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Thermosome, archaeal / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Thermosome, archaeal / 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 alpha / Thermosome subunit beta
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.737 Å
AuthorsStewart, A.G. / Smits, C. / Chaston, J.J. / 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 18, 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 1.3Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6353
Polymers120,2072
Non-polymers4271
Water0
1
B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)965,07824
Polymers961,66016
Non-polymers3,4188
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_335-x-2,-y-2,z1
crystal symmetry operation3_355-y-2,x,z1
crystal symmetry operation4_535y,-x-2,z1
crystal symmetry operation5_359-x-2,y,-z+41
crystal symmetry operation6_539x,-y-2,-z+41
crystal symmetry operation7_559y,x,-z+41
crystal symmetry operation8_339-y-2,-x-2,-z+41
2
B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules

B: Thermosome subunit beta
A: Thermosome subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,53912
Polymers480,8308
Non-polymers1,7094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_335-x-2,-y-2,z1
crystal symmetry operation3_355-y-2,x,z1
crystal symmetry operation4_535y,-x-2,z1
Buried area19590 Å2
ΔGint-127 kcal/mol
Surface area170260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.776, 145.776, 248.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
SymmetryPoint symmetry: (Schoenflies symbol: D4 (2x4 fold dihedral))
DetailsAssembly confirmed by EM and MALLS

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Components

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


Mass: 60453.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / References: UniProt: Q9V2T8
#2: Protein Thermosome subunit alpha / / Chaperonin subunit alpha / Thermophilic factor 55 alpha / TF55-alpha / Thermosome subunit 1


Mass: 59754.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / References: UniProt: Q9V2S9
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: Tris-HCl, PEG 2000, 2-propanol, strontium chloride, 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: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.73→47.69 Å / Num. obs: 14246 / % possible obs: 99.6 % / Redundancy: 19.2 % / Biso Wilson estimate: 96.66 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.679 / Rpim(I) all: 0.152 / Net I/σ(I): 6.9 / Num. measured all: 272824 / Scaling rejects: 97
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.73-4.17192.6992.27474339260.4750.60198.6
8.34-47.6917.90.094262467213810.9980.02299.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASER2.5.6phasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XCD and 3J1B

4xcd

3j1b


Resolution: 3.737→47.595 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.292 718 5.05 %
Rwork0.2474 13489 -
obs0.2496 14207 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 453.17 Å2 / Biso mean: 117.2962 Å2 / Biso min: 44.87 Å2
Refinement stepCycle: final / Resolution: 3.737→47.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7325 0 39 0 7364
Biso mean--103.55 --
Num. residues----969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057418
X-RAY DIFFRACTIONf_angle_d0.70410010
X-RAY DIFFRACTIONf_chiral_restr0.0251216
X-RAY DIFFRACTIONf_plane_restr0.0031277
X-RAY DIFFRACTIONf_dihedral_angle_d9.9192820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.737-4.02540.34031560.2972608276499
4.0254-4.43030.31051340.260926592793100
4.4303-5.07070.32981420.242126662808100
5.0707-6.38610.3331480.288927142862100
6.3861-47.59870.2291380.20932842298099

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