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- EMDB-5250: Mm-cpn deltalid with ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-5250
TitleMm-cpn deltalid with ATP
Map dataThis is the density map of Mm-cpn deltalid with ATP
Sample
  • Sample: Mm-cpn wildtype 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
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: 6.4 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 30, 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: 1.58
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.58
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3izn
  • Surface level: 1.58
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5250_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5250.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the density map of Mm-cpn deltalid with ATP
Voxel sizeX=Y=Z: 2.01 Å
Density
Contour LevelBy AUTHOR: 1.58 / Movie #1: 1.58
Minimum - Maximum-0.47899118 - 2.7328577
Average (Standard dev.)0.08731068 (±0.35313085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 289.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.012.012.01
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z289.440289.440289.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-0.4792.7330.087

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Supplemental data

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Sample components

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Entire : Mm-cpn wildtype with ATP

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

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Supramolecule #1000: Mm-cpn wildtype with ATP

SupramoleculeName: Mm-cpn wildtype 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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Gatan side entry / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: GATAN ULTRASCAN 10000 (10k x 10k) / Digitization - Scanner: OTHER

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN

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