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- PDB-4v4o: Crystal Structure of the Chaperonin Complex Cpn60/Cpn10/(ADP)7 fr... -

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Basic information

Entry
Database: PDB / ID: 4v4o
TitleCrystal Structure of the Chaperonin Complex Cpn60/Cpn10/(ADP)7 from Thermus Thermophilus
Components
  • cpn10(GroES)
  • cpn60(GroEL)
KeywordsCHAPERONE / chaperonin / groel / groes / cpn60 / cpn10 / hsp60 / hsp10 / folding / ADP / ATP
Function / homology
Function and homology information


unfolded protein binding / protein folding / protein refolding / ATP binding / cytoplasm
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / 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 / GroES-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 60 kDa chaperonin / 10 kDa chaperonin
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShimamura, T. / Koike-Takeshita, A. / Yokoyama, K. / Masui, R. / Murai, N. / Yoshida, M. / Taguchi, H. / Iwata, S.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal structure of the native chaperonin complex from Thermus thermophilus revealed unexpected asymmetry at the cis-cavity
Authors: Shimamura, T. / Koike-Takeshita, A. / Yokoyama, K. / Masui, R. / Murai, N. / Yoshida, M. / Taguchi, H. / Iwata, S.
History
DepositionMay 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1WE3, 1WF4
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cpn60(GroEL)
B: cpn60(GroEL)
C: cpn60(GroEL)
D: cpn60(GroEL)
E: cpn60(GroEL)
F: cpn60(GroEL)
G: cpn60(GroEL)
H: cpn60(GroEL)
I: cpn60(GroEL)
J: cpn60(GroEL)
K: cpn60(GroEL)
L: cpn60(GroEL)
M: cpn60(GroEL)
N: cpn60(GroEL)
O: cpn10(GroES)
P: cpn10(GroES)
Q: cpn10(GroES)
R: cpn10(GroES)
S: cpn10(GroES)
T: cpn10(GroES)
U: cpn10(GroES)
a: cpn60(GroEL)
b: cpn60(GroEL)
c: cpn60(GroEL)
d: cpn60(GroEL)
e: cpn60(GroEL)
f: cpn60(GroEL)
g: cpn60(GroEL)
h: cpn60(GroEL)
i: cpn60(GroEL)
j: cpn60(GroEL)
k: cpn60(GroEL)
l: cpn60(GroEL)
m: cpn60(GroEL)
n: cpn60(GroEL)
o: cpn10(GroES)
p: cpn10(GroES)
q: cpn10(GroES)
r: cpn10(GroES)
s: cpn10(GroES)
t: cpn10(GroES)
u: cpn10(GroES)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,782,77084
Polymers1,775,35542
Non-polymers7,41542
Water0
1
A: cpn60(GroEL)
B: cpn60(GroEL)
C: cpn60(GroEL)
D: cpn60(GroEL)
E: cpn60(GroEL)
F: cpn60(GroEL)
G: cpn60(GroEL)
H: cpn60(GroEL)
I: cpn60(GroEL)
J: cpn60(GroEL)
K: cpn60(GroEL)
L: cpn60(GroEL)
M: cpn60(GroEL)
N: cpn60(GroEL)
O: cpn10(GroES)
P: cpn10(GroES)
Q: cpn10(GroES)
R: cpn10(GroES)
S: cpn10(GroES)
T: cpn10(GroES)
U: cpn10(GroES)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)891,38542
Polymers887,67721
Non-polymers3,70721
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
a: cpn60(GroEL)
b: cpn60(GroEL)
c: cpn60(GroEL)
d: cpn60(GroEL)
e: cpn60(GroEL)
f: cpn60(GroEL)
g: cpn60(GroEL)
h: cpn60(GroEL)
i: cpn60(GroEL)
j: cpn60(GroEL)
k: cpn60(GroEL)
l: cpn60(GroEL)
m: cpn60(GroEL)
n: cpn60(GroEL)
o: cpn10(GroES)
p: cpn10(GroES)
q: cpn10(GroES)
r: cpn10(GroES)
s: cpn10(GroES)
t: cpn10(GroES)
u: cpn10(GroES)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)891,38542
Polymers887,67721
Non-polymers3,70721
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.378, 156.424, 273.153
Angle α, β, γ (deg.)82.88, 85.35, 68.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
cpn60(GroEL) / 60 kDa chaperonin


Mass: 57965.238 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P61490
#2: Protein
cpn10(GroES) / 10 kDa chaperonin


Mass: 10880.584 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P61492
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG4000, NaCl, MgCl2, DMSO, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionBiso Wilson estimate: -1.5 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5976085.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 12690 3 %RANDOM
Rwork0.239 ---
obs0.239 429625 81.3 %-
all-647041 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.5177 Å2 / ksol: 0.316722 e/Å3
Displacement parametersBiso mean: 79.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-11.2 Å2-5.95 Å2
2---1.37 Å22.42 Å2
3---1.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60415 0 224 0 60639
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 1717 2.9 %
Rwork0.376 56941 -
obs--66.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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