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- PDB-1gr5: Solution Structure of apo GroEL by Cryo-Electron microscopy -

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Basic information

Entry
Database: PDB / ID: 1gr5
TitleSolution Structure of apo GroEL by Cryo-Electron microscopy
Components60 KDA CHAPERONIN
KeywordsCHAPERONE
Function / homologyChaperonin Cpn60/TCP-1 family / GroEL-like apical domain superfamily / Chaperonins cpn60 signature. / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60 / GroEL-like equatorial domain superfamily / Chaperonin Cpn60, conserved site / TCP-1-like chaperonin intermediate domain superfamily / GroEL-GroES complex / 'de novo' protein folding ...Chaperonin Cpn60/TCP-1 family / GroEL-like apical domain superfamily / Chaperonins cpn60 signature. / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60 / GroEL-like equatorial domain superfamily / Chaperonin Cpn60, conserved site / TCP-1-like chaperonin intermediate 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 / cytoplasm / 60 kDa chaperonin / 60 kDa chaperonin
Function and homology information
Specimen sourceESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.9 Å resolution
AuthorsRanson, N.A. / Farr, G.W. / Roseman, A.M. / Gowen, B. / Fenton, W.A. / Horwich, A.L. / Saibil, H.R.
CitationJournal: Nature / Year: 1994
Title: The crystal structure of the bacterial chaperonin GroEL at 2.8 A.
Authors: K Braig / Z Otwinowski / R Hegde / D C Boisvert / A Joachimiak / A L Horwich / P B Sigler
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 14, 2001 / Release: Jan 28, 2002
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 28, 2002Structure modelrepositoryInitial release
1.1Jan 11, 2012Structure modelDatabase references / Derived calculations / Other / Structure summary / Version format compliance
1.2Oct 23, 2013Structure modelDerived calculations
1.3Aug 19, 2015Structure modelOther
1.4Aug 30, 2017Structure modelData collectionem_software_em_software.fitting_id / _em_software.image_processing_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

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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)800,63814
Polyers800,63814
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)41290
ΔGint (kcal/M)-462.2
Surface area (Å2)372230
MethodPQS

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Components

#1: Protein/peptide
60 KDA CHAPERONIN / GROEL (HSP60 CLASS) / GROEL PROTEIN / PROTEIN CPN60


Mass: 57188.410 Da / Num. of mol.: 14 / Mutation: YES / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6F6, UniProt: P0A6F5*PLUS
Compound detailsGROEL IS A HOMOOLIGOMER OF FOURTEEN SUBUNITS ARRANGED IN A DOUBLE RING STRUCTURE. ENGINEERED ...GROEL IS A HOMOOLIGOMER OF FOURTEEN SUBUNITS ARRANGED IN A DOUBLE RING STRUCTURE. ENGINEERED RESIDUE IN CHAIN A, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN B, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN B, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN C, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN C, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN D, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN D, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN E, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN E, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN F, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN F, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN G, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN G, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN H, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN H, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN I, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN I, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN J, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN J, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN K, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN K, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN L, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN L, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN M, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN M, ALA 126 TO VAL
Sequence detailsMET 1 IN ALL CHAINS HAS BEEN POST-TRANSLATIONALLY REMOVED.

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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: MOLECULAR CHAPERONEChaperone (protein) / Type: COMPLEX
Buffer solutionName: HEPES / Details: HEPES / pH: 7.5
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE
Crystal grow
*PLUS
Method: cryo-electron microscopy

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200T / Date: Feb 1, 1997
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 / Calibrated magnification: 40200 / Nominal defocus max: 1900 nm / Nominal defocus min: 800 nm
Specimen holderTemperature: 95 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 50
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1DockEMmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: CLASS AVERAGES
SymmetryPoint symmetry: D7
3D reconstructionMethod: MODEL-BASED ANGULAR REFINEMENT / Resolution: 7.9 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 8728 / Nominal pixel size: 1.82 / Actual pixel size: 1.74
Details: THE THREE DOMAINS FROM EACH SUBUNIT (PDB 1DER) WERE FITTED SEPARATELY INTO EM DENSITY OF WILD TYPE UNLIGANDED GROEL. THE MUTATIONS LISTED ARE PRESENT IN THE FITTED COORDINATES AND NOT IN THE MOLECULE WHICH GENERATED THE EM MAP. THE QUOTED RESOLUTION IS AT 3SIGMA - THE RESOLUTION AT FSC=0.5 IS 10.8A THIS ENTRY REPRESENTS THE COMPLETE BIOMOLECULE.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--X-RAY
Ref protocol: OTHER / Ref space: REAL
Atomic model buildingPDB-ID: 1DER
Least-squares processHighest resolution: 7.9 Å
Refine hist #LASTHighest resolution: 7.9 Å
Number of atoms included #LASTProtein: 52668 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 52668
Least-squares process
*PLUS
Highest resolution: 7.9 Å

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