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- EMDB-5244: Mm-cpn D386A with ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-5244
TitleMm-cpn D386A with ATP
Map dataThis is the density map of the Mm-cpn D386A mutant with ATP bound.
Sample
  • Sample: Mm-cpn D386A 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 / metal ion 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 ...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: 11.0 Å
AuthorsDouglas NR / Reissmann S / Zhang J / Chen B / Jakana J / Kumar R / Chiu W / Frydman J
CitationJournal: CELL(CAMBRIDGE,MASS.) / Year: 2011
Title: Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber.
Authors: Douglas NR / Reissmann S / Zhang J / Chen B / Jakana J / Kumar R / Chiu W / Frydman J
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: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3izh
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_5244.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the density map of the Mm-cpn D386A mutant with ATP bound.
Voxel sizeX=Y=Z: 1.81 Å
Density
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-0.4199383 - 2.34022236
Average (Standard dev.)0.07127716 (±0.25745445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 347.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.811.811.81
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z347.520347.520347.520
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-0.4202.3400.071

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Supplemental data

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Sample components

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Entire : Mm-cpn D386A with ATP

EntireName: Mm-cpn D386A with ATP
Components
  • Sample: Mm-cpn D386A with ATP
  • Protein or peptide: chaperonin

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Supramolecule #1000: Mm-cpn D386A with ATP

SupramoleculeName: Mm-cpn D386A 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 2010F
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: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN

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