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- EMDB-5245: Mm-cpn rls with ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-5245
TitleMm-cpn rls with ATP
Map dataThis is the density map of Mm-cpn rls with ATP state
Sample
  • Sample: Mm-cpn rls with ATP
  • Protein or peptide: chaperonin
KeywordsMm-cpn / maripaludis / chaperonin
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion 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 ...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: 6.7 Å
AuthorsDouglas NR / Reissmann S / Zhang J / Chen B / Jakana J / Kumar R / Chiu W / Frydman J
CitationJournal: Cell / Year: 2011
Title: Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber.
Authors: Nicholai R Douglas / Stefanie Reissmann / Junjie Zhang / Bo Chen / Joanita Jakana / Ramya Kumar / Wah Chiu / Judith Frydman /
Abstract: Group II chaperonins are ATP-dependent ring-shaped complexes that bind nonnative polypeptides and facilitate protein folding in archaea and eukaryotes. A built-in lid encapsulates substrate proteins ...Group II chaperonins are ATP-dependent ring-shaped complexes that bind nonnative polypeptides and facilitate protein folding in archaea and eukaryotes. A built-in lid encapsulates substrate proteins within the central chaperonin chamber. Here, we describe the fate of the substrate during the nucleotide cycle of group II chaperonins. The chaperonin substrate-binding sites are exposed, and the lid is open in both the ATP-free and ATP-bound prehydrolysis states. ATP hydrolysis has a dual function in the folding cycle, triggering both lid closure and substrate release into the central chamber. Notably, substrate release can occur in the absence of a lid, and lid closure can occur without substrate release. However, productive folding requires both events, so that the polypeptide is released into the confined space of the closed chamber where it folds. Our results show that ATP hydrolysis coordinates the structural and functional determinants that trigger productive folding.
History
DepositionOct 29, 2010-
Header (metadata) releaseJan 24, 2011-
Map releaseJan 24, 2011-
UpdateDec 24, 2014-
Current statusDec 24, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.28
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3izi
  • Surface level: 0.28
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5245_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5245.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the density map of Mm-cpn rls with ATP state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 192 pix.
= 255.36 Å		1.33 Å/pix.
x 192 pix.
= 255.36 Å		1.33 Å/pix.
x 192 pix.
= 255.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28 / Movie #1: 0.28
Minimum - Maximum-0.36587054 - 0.74392915
Average (Standard dev.)0.01685881 (±0.07132065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 255.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z255.360255.360255.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.3660.7440.017

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Supplemental data

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Sample components

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Entire : Mm-cpn rls with ATP

EntireName: Mm-cpn rls with ATP
Components
  • Sample: Mm-cpn rls with ATP
  • Protein or peptide: chaperonin

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Supramolecule #1000: Mm-cpn rls with ATP

SupramoleculeName: Mm-cpn rls with ATP / type: sample / ID: 1000 / Oligomeric state: 16-mer / Number unique components: 1
Molecular weightExperimental: 900 KDa / Theoretical: 900 KDa

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Macromolecule #1: chaperonin

MacromoleculeName: chaperonin / type: protein_or_peptide / ID: 1 / Name.synonym: Mm-cpn / Recombinant expression: Yes
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightExperimental: 900 KDa / Theoretical: 900 KDa
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 3200FSC
Image recordingCategory: FILM / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Scanner: OTHER
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Gatan side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN

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