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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 / Chaperone / Nucleotide-binding / Phosphoprotein
Function / homologyChaperonin Cpn60, conserved site / GroEL-like equatorial domain superfamily / Chaperonins cpn60 signature. / Chaperonin Cpn60/TCP-1 family / Chaperonin Cpn60 / TCP-1/cpn60 chaperonin family / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / GroEL-GroES complex / 'de novo' protein folding ...Chaperonin Cpn60, conserved site / GroEL-like equatorial domain superfamily / Chaperonins cpn60 signature. / Chaperonin Cpn60/TCP-1 family / Chaperonin Cpn60 / TCP-1/cpn60 chaperonin family / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / GroEL-GroES complex / 'de novo' protein folding / chaperone cofactor-dependent protein refolding / virion assembly / protein folding / response to radiation / unfolded protein binding / response to heat / protein refolding / ATPase activity / cell cycle / cell division / magnesium ion binding / membrane / ATP binding / identical protein binding / cytosol / 60 kDa chaperonin
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.7 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 18, 2008 / Release: Sep 2, 2008
RevisionDateData content typeGroupProviderType
1.0Sep 2, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jul 1, 2015Structure modelSource and taxonomy

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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
Polyers776,48714
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
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: (gene. exp.) Escherichia coli (E. coli) / Gene: groL, groEL, mopA / Plasmid name: 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 / 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 / Details: 20 mM Tris.HCl, pH 7.5, 50 mM MgCl2 / pH: 7.5
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

MicroscopyMicroscope model: 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 / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm / Cs: 1.6 mm
Specimen holderTemperature: 4 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
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
3D reconstructionMethod: EMAN, single particle / Resolution: 4.7 Å / Number of particles: 20401 / Nominal pixel size: 1.06 / Details: C7 symmetry, This entry contains CA atom only / Symmetry type: POINT
Number of atoms included #LASTProtein: 7364 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7364

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