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- EMDB-5258: Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-5258
TitleLidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state
Map dataThis is the density map of lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state.
Sample
  • Sample: Lidless D386A Mm-cpn variant
  • Protein or peptide: Methanococcus maripaludis chaperonin
KeywordsMm-cpn / Chaperonin / ATP-bound
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Thermosome, archaeal / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / 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
Similarity search - Domain/homology
Biological speciesMethanococcus maripaludis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsZhang J / Ma B / DiMaio F / Douglas NR / Joachimiak L / Baker D / Frydman J / Levitt M / Chiu W
CitationJournal: Structure / Year: 2011
Title: Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.
Authors: Junjie Zhang / Boxue Ma / Frank DiMaio / Nicholai R Douglas / Lukasz A Joachimiak / David Baker / Judith Frydman / Michael Levitt / Wah Chiu /
Abstract: Chaperonins are large ATP-driven molecular machines that mediate cellular protein folding. Group II chaperonins use their "built-in lid" to close their central folding chamber. Here we report the ...Chaperonins are large ATP-driven molecular machines that mediate cellular protein folding. Group II chaperonins use their "built-in lid" to close their central folding chamber. Here we report the structure of an archaeal group II chaperonin in its prehydrolysis ATP-bound state at subnanometer resolution using single particle cryo-electron microscopy (cryo-EM). Structural comparison of Mm-cpn in ATP-free, ATP-bound, and ATP-hydrolysis states reveals that ATP binding alone causes the chaperonin to close slightly with a ∼45° counterclockwise rotation of the apical domain. The subsequent ATP hydrolysis drives each subunit to rock toward the folding chamber and to close the lid completely. These motions are attributable to the local interactions of specific active site residues with the nucleotide, the tight couplings between the apical and intermediate domains within the subunit, and the aligned interactions between two subunits across the rings. This mechanism of structural changes in response to ATP is entirely different from those found in group I chaperonins.
History
DepositionFeb 10, 2011-
Header (metadata) releaseMay 11, 2011-
Map releaseMay 11, 2011-
UpdateMay 7, 2014-
Current statusMay 7, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j02
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5258_1.png

Downloads & links

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Map

FileDownload / File: emd_5258.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the density map of lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state.
Voxel sizeX=Y=Z: 1.42 Å
Density
Contour LevelBy EMDB: 0.02 / Movie #1: 0.075
Minimum - Maximum-0.12193819 - 0.23173273
Average (Standard dev.)0.00300522 (±0.01658083)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 340.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z340.800340.800340.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-0.1220.2320.003

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Supplemental data

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Sample components

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Entire : Lidless D386A Mm-cpn variant

EntireName: Lidless D386A Mm-cpn variant
Components
  • Sample: Lidless D386A Mm-cpn variant
  • Protein or peptide: Methanococcus maripaludis chaperonin

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Supramolecule #1000: Lidless D386A Mm-cpn variant

SupramoleculeName: Lidless D386A Mm-cpn variant / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 1 MDa / Theoretical: 1 MDa

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Macromolecule #1: Methanococcus maripaludis chaperonin

MacromoleculeName: Methanococcus maripaludis chaperonin / type: protein_or_peptide / ID: 1 / Name.synonym: Mm-cpn / Details: incubated with 1mM ATP / Number of copies: 1 / Oligomeric state: 16-mer / Recombinant expression: Yes
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightExperimental: 1 MDa / Theoretical: 1 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: vitrobot

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 112000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000
Specialist opticsEnergy filter - Name: in-column omega energy filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV
Sample stageSpecimen holder: Gatan side entry / Specimen holder model: GATAN LIQUID NITROGEN
DateSep 8, 2009
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 64 / Average electron dose: 20 e/Å2

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Image processing

CTF correctionDetails: Each CCD image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 12761

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