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- PDB-3c9v: C7 Symmetrized Structure of Unliganded GroEL at 4.7 Angstrom Reso... -

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Basic information

Entry
Database: PDB / ID: 3c9v
TitleC7 Symmetrized Structure of Unliganded GroEL at 4.7 Angstrom Resolution from CryoEM
Components60 kDa chaperonin
KeywordsCHAPERONE / GroEL / ATP-binding / Cell cycle / Cell division / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsLudtke, S.J. / Baker, M.L. / Chen, D.H. / Song, J.L. / Chuang, D. / Chiu, W.
CitationJournal: Structure / Year: 2008
Title: De novo backbone trace of GroEL from single particle electron cryomicroscopy.
Authors: Steven J Ludtke / Matthew L Baker / Dong-Hua Chen / Jiu-Li Song / David T Chuang / Wah Chiu /
Abstract: In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to approximately 4 A resolution with both D7 and C7 symmetry. Using a newly developed skeletonization ...In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to approximately 4 A resolution with both D7 and C7 symmetry. Using a newly developed skeletonization algorithm and secondary structure element identification in combination with sequence-based secondary structure prediction, we demonstrate that it is possible to achieve a de novo Calpha trace directly from a cryo-EM reconstruction. The topology of our backbone trace is completely accurate, though subtle alterations illustrate significant differences from existing crystal structures. In the map with C7 symmetry, the seven monomers in each ring are identical; however, the subunits have a subtly different structure in each ring, particularly in the equatorial domain. These differences include an asymmetric salt bridge, density in the nucleotide-binding pocket of only one ring, and small shifts in alpha helix positions. This asymmetric conformation is different from previous asymmetric structures, including GroES-bound GroEL, and may represent a "primed state" in the chaperonin pathway.
History
DepositionFeb 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 1, 2015Group: Source and taxonomy
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: 60 kDa chaperonin
B: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin
H: 60 kDa chaperonin
I: 60 kDa chaperonin
J: 60 kDa chaperonin
K: 60 kDa chaperonin
L: 60 kDa chaperonin
M: 60 kDa chaperonin
N: 60 kDa chaperonin


Theoretical massNumber of molelcules
Total (without water)776,48714
Polymers776,48714
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
60 kDa chaperonin / Protein Cpn60 / groEL protein / Coordinate model: Cα atoms only


Mass: 55463.387 Da / Num. of mol.: 14 / Fragment: residues 2-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: groL, groEL, mopA / Plasmid: pGroESL / Production host: Escherichia coli (E. coli) / Strain (production host): ESts CG-712 / References: UniProt: P0A6F5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GroEL / Type: COMPLEX / Details: 14-mer. Two back to back homo-heptameric rings.
Buffer solutionName: 20 mM Tris.HCl, pH 7.5, 50 mM MgCl2 / pH: 7.5 / Details: 20 mM Tris.HCl, pH 7.5, 50 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: ETHANE. Vitrobot, blot for 2 sec.

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FS / Date: Jan 1, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm / Cs: 1.6 mm
Specimen holderTemperature: 4 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 36 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: per micrograph
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionMethod: EMAN, single particle / Resolution: 4.7 Å / Num. of particles: 20401 / Nominal pixel size: 1.06 Å / Details: C7 symmetry, This entry contains CA atom only / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms7364 0 0 0 7364

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