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- EMDB-1202: An expanded protein folding cage in the GroEL-gp31 complex. -

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Basic information

Entry
Database: EMDB / ID: EMD-1202
TitleAn expanded protein folding cage in the GroEL-gp31 complex.
Map dataGroEL-gp31-ADP 3D density map. The box size is 192,192,192 and the map is centred at 0,0,0.
Sample
  • Sample: GroEL-ADP-gp31
  • Protein or peptide: GroEL
  • Protein or peptide: gp31
  • Ligand: ADPAdenosine diphosphate
Function / homology
Function and homology information


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 ...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 / Chaperonin Cpn60/GroEL / GroEL-like equatorial 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsClare DK / Bakkes PJ / van Heerikhuizen H / van der Vies SM / Saibil HR
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
DepositionFeb 15, 2006-
Header (metadata) releaseMar 9, 2006-
Map releaseMar 9, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2cgt
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1202.gif

Downloads & links

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Map

FileDownload / File: emd_1202.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGroEL-gp31-ADP 3D density map. The box size is 192,192,192 and the map is centred at 0,0,0.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.4 Å/pix.
x 192 pix.
= 268.8 Å		1.4 Å/pix.
x 192 pix.
= 268.8 Å		1.4 Å/pix.
x 192 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.452 / Movie #1: 0.6
Minimum - Maximum-1.62214 - 3.4708
Average (Standard dev.)0.0529811 (±0.231513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 268.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S213
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-1.6223.4710.053

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Supplemental data

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Sample components

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Entire : GroEL-ADP-gp31

EntireName: GroEL-ADP-gp31
Components
  • Sample: GroEL-ADP-gp31
  • Protein or peptide: GroEL
  • Protein or peptide: gp31
  • Ligand: ADPAdenosine diphosphate

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Supramolecule #1000: GroEL-ADP-gp31

SupramoleculeName: GroEL-ADP-gp31 / type: sample / ID: 1000
Oligomeric state: heptamer of gp31 and a tetradecamer of GroEL
Number unique components: 3
Molecular weightExperimental: 900 KDa / Theoretical: 900 KDa / Method: Mass spectrometry

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Name.synonym: chaperonin / Number of copies: 1 / Oligomeric state: tetradecamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: E. coli MC1009 and BL21 / synonym: E. coli / Location in cell: cytoplasm
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pSL6
SequenceGO: protein binding / InterPro: Chaperonin Cpn60/GroEL

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Macromolecule #2: gp31

MacromoleculeName: gp31 / type: protein_or_peptide / ID: 2 / Name.synonym: co-chaperonin / Number of copies: 1 / Oligomeric state: heptamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E. coli / Location in cell: cytoplasm
Molecular weightExperimental: 100 KDa / Theoretical: 100 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pAR1
SequenceInterPro: INTERPRO: IPR011597

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Macromolecule #3: ADP

MacromoleculeName: ADP / type: ligand / ID: 3 / Name.synonym: nucleotide / Number of copies: 14 / Oligomeric state: monomer / Recombinant expression: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.4 / Details: 20mM Tris-HCL, 10mM MgCl, 10mM KCl
GridDetails: 300 mesh copper grid - holey carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home made / Timed resolved state: Vitrified after 10 minute incubation
Method: The 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

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.3 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: single tilt / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism corrected at 150kX
DateSep 28, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 28 / Average electron dose: 15 e/Å2 / Od range: 1 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: full correction on 2D class averages
Final two d classificationNumber classes: 523
Final angle assignmentDetails: theta 15 (88-103), phi 51(0-51)
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider and imagic
Details: final maps were calculated from 523 averaged angle bins
Number images used: 10300
DetailsThe particles were hand picked

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Atomic model buiding 1

Initial model(PDB ID:

1aon

,

1g31

)
SoftwareName: URO
DetailsProtocol: density correlation. the 3 domains of two GroEL subunits and a single gp31 subunit were docked as rigid bodies into the density map
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation
Output model

PDB-2cgt:
GROEL-ADP-gp31 COMPLEX

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