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- EMDB-5645: Independent reconstruction of Mm-cpn cryo-EM density map from hal... -

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Basic information

Entry
Database: EMDB / ID: EMD-5645
TitleIndependent reconstruction of Mm-cpn cryo-EM density map from half dataset in the closed state (Training map)
Map dataIndependent reconstruction of Mm-cpn cryo-EM density map from half dataset in the closed state (Training map)
Sample
  • Sample: Mm-cpn with 1mM ATP/AlFx
  • Protein or peptide: chaperonin
Keywordsmodeling / independent reconstruction / cryo-EM model validation
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: 4.6 Å
AuthorsDiMaio F / Zhang J / Chiu W / Baker D
CitationJournal: Protein Sci / Year: 2013
Title: Cryo-EM model validation using independent map reconstructions.
Authors: Frank DiMaio / Junjie Zhang / Wah Chiu / David Baker /
Abstract: An increasing number of cryo-electron microscopy (cryo-EM) density maps are being generated with suitable resolution to trace the protein backbone and guide sidechain placement. Generating and ...An increasing number of cryo-electron microscopy (cryo-EM) density maps are being generated with suitable resolution to trace the protein backbone and guide sidechain placement. Generating and evaluating atomic models based on such maps would be greatly facilitated by independent validation metrics for assessing the fit of the models to the data. We describe such a metric based on the fit of atomic models with independent test maps from single particle reconstructions not used in model refinement. The metric provides a means to determine the proper balance between the fit to the density and model energy and stereochemistry during refinement, and is likely to be useful in determining values of model building and refinement metaparameters quite generally.
History
DepositionMay 1, 2013-
Header (metadata) releaseMay 29, 2013-
Map releaseMay 29, 2013-
UpdateJun 12, 2013-
Current statusJun 12, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.27
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.27
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j3x
  • Surface level: 0.27
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5645_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5645.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIndependent reconstruction of Mm-cpn cryo-EM density map from half dataset in the closed state (Training map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 192 pix.
= 249.6 Å		1.3 Å/pix.
x 192 pix.
= 249.6 Å		1.3 Å/pix.
x 192 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27 / Movie #1: 0.27
Minimum - Maximum-0.60766435 - 0.93535215
Average (Standard dev.)0.01417639 (±0.07355431)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.6080.9350.014

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Supplemental data

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Sample components

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Entire : Mm-cpn with 1mM ATP/AlFx

EntireName: Mm-cpn with 1mM ATP/AlFx
Components
  • Sample: Mm-cpn with 1mM ATP/AlFx
  • Protein or peptide: chaperonin

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Supramolecule #1000: Mm-cpn with 1mM ATP/AlFx

SupramoleculeName: Mm-cpn with 1mM ATP/AlFx / type: sample / ID: 1000 / Oligomeric state: 16-mer / Number unique components: 1
Molecular weightExperimental: 960 KDa / Theoretical: 960 KDa

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Macromolecule #1: chaperonin

MacromoleculeName: chaperonin / type: protein_or_peptide / ID: 1 / Name.synonym: Mm-cpn / Number of copies: 16 / Oligomeric state: 16-mer / Recombinant expression: Yes
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightExperimental: 960 KDa / Theoretical: 960 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: FEI VITROBOT MARK III / Method: Blot once for 3 seconds.

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Specialist opticsEnergy filter - Name: in-column omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV
DateFeb 29, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 112000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000
Sample stageSpecimen holder: side-entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 22571

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