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- PDB-3ko1: Cystal structure of thermosome from Acidianus tengchongensis strain S5 -

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Basic information

Entry
Database: PDB / ID: 3ko1
TitleCystal structure of thermosome from Acidianus tengchongensis strain S5
ComponentsChaperonin
KeywordsCHAPERONE / 9-fold symmetry / double ring / ATP hydrolase / Nucleotide-binding
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / 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 / Chaperonin
Similarity search - Component
Biological speciesAcidianus tengchongensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsHuo, Y. / Zhang, K. / Hu, Z. / Wang, L. / Zhai, Y. / Zhou, Q. / Lander, G. / He, Y. / Zhu, J. / Xu, W. ...Huo, Y. / Zhang, K. / Hu, Z. / Wang, L. / Zhai, Y. / Zhou, Q. / Lander, G. / He, Y. / Zhu, J. / Xu, W. / Dong, Z. / Sun, F.
CitationJournal: Structure / Year: 2010
Title: Crystal structure of group II chaperonin in the open state.
Authors: Yanwu Huo / Zhongjun Hu / Kai Zhang / Li Wang / Yujia Zhai / Qiangjun Zhou / Gabe Lander / Jiang Zhu / Yongzhi He / Xiaoyun Pang / Wei Xu / Mark Bartlam / Zhiyang Dong / Fei Sun /
Abstract: Thermosomes are group II chaperonins responsible for protein refolding in an ATP-dependent manner. Little is known regarding the conformational changes of thermosomes during their functional cycle ...Thermosomes are group II chaperonins responsible for protein refolding in an ATP-dependent manner. Little is known regarding the conformational changes of thermosomes during their functional cycle due to a lack of high-resolution structure in the open state. Here, we report the first complete crystal structure of thermosome (rATcpnβ) in the open state from Acidianus tengchongensis. There is a ∼30° rotation of the apical and lid domains compared with the previous closed structure. Besides, the structure reveals a conspicuous hydrophobic patch in the lid domain, and residues locating in this patch are conserved across species. Both the closed and open forms of rATcpnβ were also reconstructed by electron microscopy (EM). Structural fitting revealed the detailed conformational change from the open to the closed state. Structural comparison as well as protease K digestion indicated only ATP binding without hydrolysis does not induce chamber closure of thermosome.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
E: Chaperonin
F: Chaperonin
G: Chaperonin
H: Chaperonin
I: Chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,49018
Polymers537,6459
Non-polymers3,8459
Water0
1
A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
E: Chaperonin
F: Chaperonin
G: Chaperonin
H: Chaperonin
I: Chaperonin
hetero molecules

A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
E: Chaperonin
F: Chaperonin
G: Chaperonin
H: Chaperonin
I: Chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,082,98036
Polymers1,075,29018
Non-polymers7,69018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area52950 Å2
ΔGint-253 kcal/mol
Surface area382030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.674, 283.042, 160.750
Angle α, β, γ (deg.)90.00, 133.90, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I

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Components

#1: Protein
Chaperonin /


Mass: 59738.344 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus tengchongensis (archaea) / Strain: S5 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta-gami / References: UniProt: Q877H2
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 9 / 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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-Hcl, 1.15M Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 10, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 76576 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 7.4
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3429 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0088refinement
CNS2.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q3R

1q3r


Resolution: 3.7→48.39 Å / SU B: 47.548 / SU ML: 0.649 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.814 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3825 5 %RANDOM
Rwork0.277 ---
obs0.277 76142 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 123.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.511 Å20 Å2-28.794 Å2
2--24.962 Å20 Å2
3----29.473 Å2
Refinement stepCycle: LAST / Resolution: 3.7→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34641 0 243 0 34884

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