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- PDB-1gru: SOLUTION STRUCTURE OF GROES-ADP7-GROEL-ATP7 COMPLEX BY CRYO-EM -

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Basic information

Entry
Database: PDB / ID: 1gru
TitleSOLUTION STRUCTURE OF GROES-ADP7-GROEL-ATP7 COMPLEX BY CRYO-EM
Components
  • GROEL
  • GROES
KeywordsCHAPERONE / CHAPERONIN / HSP60 / GROEL-GROES / MOLECULAR CHAPERONE / ADP
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 / 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
Co-chaperonin GroES / Chaperonin GroEL / Chaperonin GroEL / Co-chaperonin GroES
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsRanson, N.A. / Farr, G.W. / Roseman, A.M. / Gowen, B. / Fenton, W.A. / Horwich, A.L. / Saibil, H.R.
CitationJournal: Cell / Year: 2001
Title: ATP-bound states of GroEL captured by cryo-electron microscopy.
Authors: N A Ranson / G W Farr / A M Roseman / B Gowen / W A Fenton / A L Horwich / H R Saibil /
Abstract: The chaperonin GroEL drives its protein-folding cycle by cooperatively binding ATP to one of its two rings, priming that ring to become folding-active upon GroES binding, while simultaneously ...The chaperonin GroEL drives its protein-folding cycle by cooperatively binding ATP to one of its two rings, priming that ring to become folding-active upon GroES binding, while simultaneously discharging the previous folding chamber from the opposite ring. The GroEL-ATP structure, determined by cryo-EM and atomic structure fitting, shows that the intermediate domains rotate downward, switching their intersubunit salt bridge contacts from substrate binding to ATP binding domains. These observations, together with the effects of ATP binding to a GroEL-GroES-ADP complex, suggest structural models for the ATP-induced reduction in affinity for polypeptide and for cooperativity. The model for cooperativity, based on switching of intersubunit salt bridge interactions around the GroEL ring, may provide general insight into cooperativity in other ring complexes and molecular machines.
History
DepositionDec 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
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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Structure viewerMolecule:
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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: GROES
P: GROES
Q: GROES
R: GROES
S: GROES
T: GROES
U: GROES


Theoretical massNumber of molelcules
Total (without water)874,45421
Polymers874,45421
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32680 Å2
ΔGint-336.8 kcal/mol
Surface area356330 Å2
MethodPQS

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Components

#1: Protein
GROEL /


Mass: 57260.504 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P06139, UniProt: P0A6F5*PLUS
#2: Protein
GROES /


Mass: 10400.938 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05380, UniProt: P0A6F9*PLUS
Compound detailsCRYO-EM MAP OF GROEL-GROES COMPLEX WITH ADP IN THE (CIS)RING WITH GROES BOUND AND ATP IN THE OPEN ...CRYO-EM MAP OF GROEL-GROES COMPLEX WITH ADP IN THE (CIS)RING WITH GROES BOUND AND ATP IN THE OPEN (TRANS) RING.

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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 (C7) / Type: COMPLEX
Buffer solutionName: HEPES / pH: 7.5 / Details: HEPES
SpecimenConc.: 1 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

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jul 1, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Specimen holderTemperature: 95 K / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1Omodel fittingManual fitting
2SPIDER3D reconstruction
CTF correctionDetails: CLASS AVERAGES
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionMethod: MODEL BASED ANGULAR REFINEMENT / Resolution: 12.5 Å / Num. of particles: 1448 / Nominal pixel size: 2.8 Å / Actual pixel size: 2.8 Å
Details: ATOMIC COORDINATES FROM 1AON FITTED BY HAND. CIS RING FITTED WHOLE. TRANS EQUATORIAL AND INTERMEDIATE DOMAINS ALSO FITTED AS 7MER. A SINGLE TRANS APICAL WAS FITTED BY HAND AND THEN THE OTHER ...Details: ATOMIC COORDINATES FROM 1AON FITTED BY HAND. CIS RING FITTED WHOLE. TRANS EQUATORIAL AND INTERMEDIATE DOMAINS ALSO FITTED AS 7MER. A SINGLE TRANS APICAL WAS FITTED BY HAND AND THEN THE OTHER 6 POSITIONS CREATED FROM SYMMETRY.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--BY HAND REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 1GRU
RefinementHighest resolution: 12.5 Å
Refinement stepCycle: LAST / Highest resolution: 12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58688 0 0 0 58688

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