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- PDB-1aon: CRYSTAL STRUCTURE OF THE ASYMMETRIC CHAPERONIN COMPLEX GROEL/GROE... -

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Basic information

Entry
Database: PDB / ID: 1aon
TitleCRYSTAL STRUCTURE OF THE ASYMMETRIC CHAPERONIN COMPLEX GROEL/GROES/(ADP)7
Components
  • GROEL/GROES COMPLEX
  • GROEL
KeywordsCOMPLEX (GROEL/GROES) / COMPLEX (GROEL-GROES) / CHAPERONIN ASSISTED PROTEIN FOLDING / COMPLEX (GROEL-GROES) complex
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein-folding chaperone binding / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / metal ion binding / cytosol
Similarity search - Function
10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroEL ...10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroEL / GroEL / 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 / 3-Layer(bba) Sandwich / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chaperonin GroEL / Co-chaperonin GroES
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsXu, Z. / Horwich, A.L. / Sigler, P.B.
Citation
Journal: Nature / Year: 1997
Title: The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex.
Authors: Z Xu / A L Horwich / P B Sigler /
Abstract: Chaperonins assist protein folding with the consumption of ATP. They exist as multi-subunit protein assemblies comprising rings of subunits stacked back to back. In Escherichia coli, asymmetric ...Chaperonins assist protein folding with the consumption of ATP. They exist as multi-subunit protein assemblies comprising rings of subunits stacked back to back. In Escherichia coli, asymmetric intermediates of GroEL are formed with the co-chaperonin GroES and nucleotides bound only to one of the seven-subunit rings (the cis ring) and not to the opposing ring (the trans ring). The structure of the GroEL-GroES-(ADP)7 complex reveals how large en bloc movements of the cis ring's intermediate and apical domains enable bound GroES to stabilize a folding chamber with ADP confined to the cis ring. Elevation and twist of the apical domains double the volume of the central cavity and bury hydrophobic peptide-binding residues in the interface with GroES, as well as between GroEL subunits, leaving a hydrophilic cavity lining that is conducive to protein folding. An inward tilt of the cis equatorial domain causes an outward tilt in the trans ring that opposes the binding of a second GroES. When combined with new functional results, this negative allosteric mechanism suggests a model for an ATP-driven folding cycle that requires a double toroid.
#1: Journal: Nature / Year: 1997
Title: Distinct Actions of Cis and Trans ATP within the Double Ring of the Chaperonin Groel
Authors: Rye, H.S. / Burston, S.G. / Fenton, W.A. / Beechem, J.M. / Xu, Z. / Sigler, P.B. / Horwich, A.L.
History
DepositionJul 8, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_asym_id / _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_asym_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 / _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

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Assembly

Deposited unit
A: GROEL
B: GROEL
C: GROEL
D: GROEL
E: GROEL
F: GROEL
G: GROEL
H: GROEL
I: GROEL
J: GROEL
K: GROEL
L: GROEL
M: GROEL
N: GROEL
O: GROEL/GROES COMPLEX
P: GROEL/GROES COMPLEX
Q: GROEL/GROES COMPLEX
R: GROEL/GROES COMPLEX
S: GROEL/GROES COMPLEX
T: GROEL/GROES COMPLEX
U: GROEL/GROES COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)877,61435
Polymers874,45421
Non-polymers3,16114
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area69480 Å2
ΔGint-486 kcal/mol
Surface area314810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)255.260, 265.250, 184.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.62341, 0.781886, -0.003757), (-0.781887, 0.623418, 0.001742), (0.003705, 0.001852, 0.999991)70.3607, 42.435, 0.086
2given(-0.224043, 0.974579, -0.000348), (-0.974576, -0.224041, 0.002662), (0.002516, 0.000936, 0.999996)147.39571, 13.9247, 0.0299
3given(-0.899764, 0.436376, -0.00092), (-0.436376, -0.899764, 4.6E-5), (-0.000808, 0.000443, 1)173.0845, -63.4226, 0.1381
4given(-0.9028, -0.430056, -0.001948), (0.430051, -0.902801, 0.002556), (-0.002858, 0.00147, 0.999995)128.82761, -132.13429, 0.3881
5given(-0.219823, -0.97554, -0.000496), (0.975537, -0.219824, 0.002092), (-0.00215, -2.5E-5, 0.999998)46.6125, -140.57449, 0.3558
6given(0.629141, -0.777284, 0.003401), (0.777283, 0.629148, 0.001725), (-0.00348, 0.001558, 0.999993)-10.639, -81.0987, 0.4239
7given(0.621053, 0.783687, 0.011271), (-0.783756, 0.621059, 0.003404), (-0.004332, -0.010947, 0.999931)70.319, 42.266, -0.6474
8given(-0.225521, 0.974219, 0.006096), (-0.974232, -0.225494, -0.004862), (-0.003362, -0.007035, 0.99997)147.35561, 13.779, -0.2763
9given(-0.901799, 0.432098, -0.006988), (-0.432057, -0.901821, -0.006691), (-0.009193, -0.003015, 0.999953)173.09261, -63.8633, 1.0467
10given(-0.900517, -0.434636, -0.012671), (0.43466, -0.900594, 0.000946), (-0.011823, -0.004656, 0.999919)128.4648, -132.42599, 1.3282
11given(-0.214381, -0.976732, 0.006021), (0.976711, -0.214314, 0.010216), (-0.008688, 0.00807, 0.99993)45.8922, -140.565, 0.8028
12given(0.62578, -0.779979, 0.005728), (0.779991, 0.62579, 6.1E-5), (-0.003632, 0.00443, 0.999984)-10.602, -81.3088, 0.2378
13given(0.635136, 0.772132, 0.020375), (-0.772336, 0.635204, 0.003764), (-0.010036, -0.018127, 0.999785)71.0063, 42.903, -0.4356
14given(-0.214346, 0.976563, 0.019492), (-0.976756, -0.21434, -0.002426), (0.001809, -0.019559, 0.999807)148.6774, 14.3745, -1.4739
15given(-0.899081, 0.437601, 0.012614), (-0.437629, -0.899155, 0.000547), (0.011581, -0.005028, 0.99992)174.2243, -63.354, -1.2723
16given(-0.905937, -0.423163, 0.014537), (0.423306, -0.905946, 0.00859), (0.009535, 0.013935, 0.999857)130.58031, -130.89951, -0.0659
17given(-0.228903, -0.973253, 0.019526), (0.973444, -0.228919, 0.001443), (0.003065, 0.019338, 0.999808)48.8816, -140.22121, 0.654
18given(0.613988, -0.789067, 0.019793), (0.789305, 0.613914, -0.010322), (-0.004007, 0.02196, 0.999751)-8.023, -83.2415, 1.1173

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Components

#1: Protein
GROEL / / 60 KD CHAPERONIN / PROTEIN CPN60


Mass: 57260.504 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 / Cell line: BL21 / Gene: GROE / Plasmid: IQ-TRC / Gene (production host): GROEL / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P0A6F5
#2: Protein
GROEL/GROES COMPLEX / 10 KD CHAPERONIN / PROTEIN CPN10


Mass: 10400.938 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 / Cell line: BL21 / Gene: GROE / Plasmid: PET11A / Species (production host): Escherichia coli / Gene (production host): GROES / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6F9
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 7 / 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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growpH: 5.5
Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG3000, 0.25M SODIUM GLUTAMATE, 100MM CACODYLIC ACID, PH 5.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %PEG30001reservoir
20.25 Msodium glutamate1reservoir
3100 mMcacodylate1reservoir
46 %PEG30001drop
50.125 Msodium glutamate1drop
650 mMcacodylate1drop
77.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromator: TWO CRYSTAL NON-DISPERSIVE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3→99 Å / Num. obs: 242684 / % possible obs: 96.7 % / Redundancy: 3.3 % / Rsym value: 0.121 / Net I/σ(I): 9.1
Reflection shellResolution: 3→3.14 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.53 / % possible all: 91.2
Reflection
*PLUS
Rmerge(I) obs: 0.121
Reflection shell
*PLUS
% possible obs: 91.2 % / Num. unique obs: 28317 / Rmerge(I) obs: 0.53

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OEL

1oel


Resolution: 3→40 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUE 526 - 547 IN EACH GROEL CHAIN ARE ABSENT FROM THE MODEL BECAUSE THE ELECTRON DENSITY FOR THESE RESIDUES COULD NOT BE INTERPRETED. ARG 197, PHE 204, LYS 225, LYS 226, SER 228 - GLU ...Details: RESIDUE 526 - 547 IN EACH GROEL CHAIN ARE ABSENT FROM THE MODEL BECAUSE THE ELECTRON DENSITY FOR THESE RESIDUES COULD NOT BE INTERPRETED. ARG 197, PHE 204, LYS 225, LYS 226, SER 228 - GLU 232, GLU 238 IN CHAINS A - G ARE MODELLED AS ALANINE.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 9846 5 %RANDOM
Rwork0.248 ---
obs0.248 198459 79.7 %-
Displacement parametersBiso mean: 61.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.83 Å20 Å20 Å2
2--12.27 Å20 Å2
3----27.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58688 0 196 0 58884
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.472
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.711.5
X-RAY DIFFRACTIONx_mcangle_it4.322
X-RAY DIFFRACTIONx_scbond_it4.042
X-RAY DIFFRACTIONx_scangle_it62.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.389 827 5 %
Rwork0.356 16487 -
obs--56 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPARHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMTOPH19.PEP
X-RAY DIFFRACTION3PARAM19.ION
Software
*PLUS
Name: X-PLOR / Version: 3.861 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71

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