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- PDB-2cgt: GROEL-ADP-gp31 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2cgt
TitleGROEL-ADP-gp31 COMPLEX
Components
  • 60 KDA GROEL
  • CAPSID ASSEMBLY PROTEIN GP31
KeywordsCHAPERONE / CHAPERONIN / CELL CYCLE / CELL DIVISION / CAPSID ASSEMBLY / EARLY PROTEIN
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / viral capsid assembly / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding ...GroEL-GroES complex / chaperonin ATPase / viral capsid assembly / 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 refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
Bacteriophage T4, Gp31, chaperonin-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 ...Bacteriophage T4, Gp31, chaperonin-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
Similarity search - Domain/homology
Chaperonin GroEL / Capsid assembly protein Gp31
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
BACTERIOPHAGE T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsClare, D.K. / Bakkes, P.J. / van Heerikhuizen, H. / van der Vies, S.M. / Saibil, H.R.
CitationJournal: J Mol Biol / Year: 2006
Title: An expanded protein folding cage in the GroEL-gp31 complex.
Authors: Daniel K Clare / Patrick J Bakkes / Harm van Heerikhuizen / Saskia M van der Vies / Helen R Saibil /
Abstract: Bacteriophage T4 produces a GroES analogue, gp31, which cooperates with the Escherichia coli GroEL to fold its major coat protein gp23. We have used cryo-electron microscopy and image processing to ...Bacteriophage T4 produces a GroES analogue, gp31, which cooperates with the Escherichia coli GroEL to fold its major coat protein gp23. We have used cryo-electron microscopy and image processing to obtain three-dimensional structures of the E.coli chaperonin GroEL complexed with gp31, in the presence of both ATP and ADP. The GroEL-gp31-ADP map has a resolution of 8.2 A, which allows accurate fitting of the GroEL and gp31 crystal structures. Comparison of this fitted structure with that of the GroEL-GroES-ADP structure previously determined by cryo-electron microscopy shows that the folding cage is expanded. The enlarged volume for folding is consistent with the size of the bacteriophage coat protein gp23, which is the major substrate of GroEL-gp31 chaperonin complex. At 56 kDa, gp23 is close to the maximum size limit of a polypeptide that is thought to fit inside the GroEL-GroES folding cage.
History
DepositionMar 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2006Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id
Revision 1.3Oct 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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Assembly

Deposited unit
A: 60 KDA GROEL
B: 60 KDA GROEL
C: 60 KDA GROEL
D: 60 KDA GROEL
E: 60 KDA GROEL
F: 60 KDA GROEL
G: 60 KDA GROEL
H: 60 KDA GROEL
I: 60 KDA GROEL
J: 60 KDA GROEL
K: 60 KDA GROEL
L: 60 KDA GROEL
M: 60 KDA GROEL
N: 60 KDA GROEL
O: CAPSID ASSEMBLY PROTEIN GP31
P: CAPSID ASSEMBLY PROTEIN GP31
Q: CAPSID ASSEMBLY PROTEIN GP31
R: CAPSID ASSEMBLY PROTEIN GP31
S: CAPSID ASSEMBLY PROTEIN GP31
T: CAPSID ASSEMBLY PROTEIN GP31
U: CAPSID ASSEMBLY PROTEIN GP31


Theoretical massNumber of molelcules
Total (without water)886,29121
Polymers886,29121
Non-polymers00
Water0
1


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

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Components

#1: Protein
60 KDA GROEL / PROTEIN CPN60 / GROEL PROTEIN


Mass: 57260.504 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: A TETRADECAMER ARRANGED AS TWO BACK-TO-BACK HEPTAMERS
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PSL6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6F5
#2: Protein
CAPSID ASSEMBLY PROTEIN GP31


Mass: 12091.999 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: HEPTAMER / Source: (gene. exp.) BACTERIOPHAGE T4 (virus) / Plasmid: PAR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1009 / References: UniProt: P17313
Sequence detailsRESIDUES 23-46 HAVE BEEN REMOVED FROM THE GP31 STRUCTURE AS THEY WERE IN A DISTORTED CONFORMATION ...RESIDUES 23-46 HAVE BEEN REMOVED FROM THE GP31 STRUCTURE AS THEY WERE IN A DISTORTED CONFORMATION IN THE ORIGINAL CRYSTAL STRUCTURE.

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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-GP31-ADP / Type: COMPLEX
Buffer solutionName: 20MM TRIS-HCL, 10MM MGCL, 10MM KCL / pH: 7.4 / Details: 20MM TRIS-HCL, 10MM MGCL, 10MM KCL
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: GRIDS WERE BLOTED FOR 2-3 SECONDS AND THEN LEFT TO EQUILIBRATE FOR 2-3 SECONDS AND THEN PLUNGED INTO LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Sep 28, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3300 nm / Nominal defocus min: 1300 nm / Cs: 2 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 28
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1IMAGIC3D reconstruction
2SPIDER3D reconstruction
CTF correctionDetails: FULL CORRECTION ON 2D CLASS AVERAGES
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 8.2 Å / Num. of particles: 10300 / Nominal pixel size: 1.4 Å / Actual pixel size: 1.4 Å
Details: THE 3 DOMAINS OF TWO GROEL SUBUNITS AND A SINGLE GP31 SUBUNIT WERE DOCKED AS RIGID BODIES INTO THE DENSITY MAP
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-ID
11A0N

1a0n

1
21G31

1g31

1
RefinementHighest resolution: 8.2 Å
Refinement stepCycle: LAST / Highest resolution: 8.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57953 0 0 0 57953

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