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- EMDB-1588: Cryo-EM structure of the native GroEL-GroES complex from Thermus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1588
TitleCryo-EM structure of the native GroEL-GroES complex from Thermus thermophilus encapsulating substrate inside the cavity.
Map dataa EM-map of the GroEL-GroES-ADP-peptide complex from Thermus thermophilus
Sample
  • Sample: The GroEL-GroES-ADP-peptide complex from Thermus thermophilus
  • Protein or peptide: GroEL
  • Protein or peptide: GroES
  • Protein or peptide: peptide
  • Ligand: ADP
Biological speciesThermus thermophilus (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.0 Å
AuthorsKanno R / Koike-Takeshita A / Yokoyama K / Taguchi H / Mitsuoka K
CitationJournal: Structure / Year: 2009
Title: Cryo-EM structure of the native GroEL-GroES complex from thermus thermophilus encapsulating substrate inside the cavity.
Authors: Ryo Kanno / Ayumi Koike-Takeshita / Ken Yokoyama / Hideki Taguchi / Kaoru Mitsuoka /
Abstract: The chaperonin GroEL interacts with various proteins, leading them to adopt their correct conformations with the aid of GroES and ATP. The actual mechanism is still being debated. In this study, by ...The chaperonin GroEL interacts with various proteins, leading them to adopt their correct conformations with the aid of GroES and ATP. The actual mechanism is still being debated. In this study, by use of cryo-electron microscopy, we determined the solution structure of the Thermus thermophilus GroEL-GroES complex encapsulating its substrate proteins. We observed the averaged density of substrate proteins in the center of the GroEL-GroES cavity. The position of the averaged substrate density in the cavity suggested a repulsive interaction between a majority of the substrate proteins and the interior wall of the cavity, which is suitable for substrate release. In addition, we observed a distortion of the cis-GroEL ring, especially at the position near the substrate, which indicated that the interaction between the encapsulated proteins and the GroEL ring results in an adjustment in the cavity's shape to accommodate the substrate.
History
DepositionDec 16, 2008-
Header (metadata) releaseJan 6, 2009-
Map releaseApr 1, 2009-
UpdateDec 25, 2013-
Current statusDec 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v4o
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1588.gif

Downloads & links

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Map

FileDownload / File: emd_1588.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationa EM-map of the GroEL-GroES-ADP-peptide complex from Thermus thermophilus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 224 pix.
= 365.12 Å		1.63 Å/pix.
x 224 pix.
= 365.12 Å		1.63 Å/pix.
x 224 pix.
= 365.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.05 / Movie #1: 0.04
Minimum - Maximum-0.168899 - 0.164869
Average (Standard dev.)-0.000363028 (±0.0167269)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 365.12 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z365.120365.120365.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.1690.165-0.000

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Supplemental data

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Sample components

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Entire : The GroEL-GroES-ADP-peptide complex from Thermus thermophilus

EntireName: The GroEL-GroES-ADP-peptide complex from Thermus thermophilus
Components
  • Sample: The GroEL-GroES-ADP-peptide complex from Thermus thermophilus
  • Protein or peptide: GroEL
  • Protein or peptide: GroES
  • Protein or peptide: peptide
  • Ligand: ADP

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Supramolecule #1000: The GroEL-GroES-ADP-peptide complex from Thermus thermophilus

SupramoleculeName: The GroEL-GroES-ADP-peptide complex from Thermus thermophilus
type: sample / ID: 1000 / Number unique components: 4
Molecular weightTheoretical: 870 KDa

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Name.synonym: chaperonin / Recombinant expression: Yes
Source (natural)Organism: Thermus thermophilus (bacteria)

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Macromolecule #2: GroES

MacromoleculeName: GroES / type: protein_or_peptide / ID: 2 / Name.synonym: co-chaperonin / Recombinant expression: Yes
Source (natural)Organism: Thermus thermophilus (bacteria)

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Macromolecule #4: peptide

MacromoleculeName: peptide / type: protein_or_peptide / ID: 4 / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)

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Macromolecule #3: ADP

MacromoleculeName: ADP / type: ligand / ID: 3 / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)

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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

VitrificationCryogen name: METHANE / Instrument: OTHER

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Electron microscopy #1

Microscopy ID1
MicroscopeJEOL 3200FSC
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 336 / Bits/pixel: 12
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: JEOL 3200FSC CRYOHOLDER

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Electron microscopy #2

Microscopy ID2
MicroscopeJEOL 2200FS
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 336 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

CTF correctionDetails: CTF correction with wiener fIlter when 2D averaging
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC

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Atomic model buiding 1

Initial modelPDB ID:

1wf4
PDB Unreleased entry

RefinementSpace: REAL

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