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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: 5258
TitleLidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state
KeywordsMm-cpn / Chaperonin / ATP-bound
SampleLidless D386A Mm-cpn variant
SourceMethanococcus maripaludis / archaea / メタノコッカス・マリパルディス
Map dataThis is the density map of lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state.
Methodsingle particle reconstruction, at 8 A resolution
AuthorsZhang J / Ma B / DiMaio F / Douglas NR / Joachimiak L / Baker D / Frydman J / Levitt M / Chiu W
CitationStructure, 2011, 19, 633-639

Structure, 2011, 19, 633-639 StrPapers
Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.
Junjie Zhang / Boxue Ma / Frank DiMaio / Nicholai R Douglas / Lukasz A Joachimiak / David Baker / Judith Frydman / Michael Levitt / Wah Chiu

DateDeposition: Feb 10, 2011 / Header (metadata) release: May 11, 2011 / Map release: May 11, 2011 / Last update: Feb 10, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.075
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.075
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3j02
  • Surface level: 0.075
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_5258.map.gz (map file in CCP4 format, 54001 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.42 A/pix
= 340.8 A
240 pix
1.42 A/pix
= 340.8 A
240 pix
1.42 A/pix
= 340.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.42 A
Density
Contour Level:0.02 (by emdb), 0.075 (movie #1):
Minimum - Maximum-0.12193819 - 0.23173273
Average (Standard dev.)0.00300522 (0.01658083)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin-120-120-120
Limit119119119
Spacing240240240
CellA=B=C: 340.8 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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 / Number of components: 1
MassTheoretical: 1000 kDa / Experimental: 1000 kDa

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Component #1: protein, Methanococcus maripaludis chaperonin

ProteinName: Methanococcus maripaludis chaperonin / a.k.a: Mm-cpn / Oligomeric Details: 16-mer / Details: incubated with 1mM ATP / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 1000 kDa / Experimental: 1000 kDa
SourceSpecies: Methanococcus maripaludis / archaea / メタノコッカス・マリパルディス
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Details: Vitrification instrument: vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS / Date: Sep 8, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal), 112000 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm / Energy filter: in-column omega energy filter / Energy window: 0-10 eV
Specimen HolderHolder: Gatan side entry / Model: GATAN LIQUID NITROGEN
CameraDetector: GENERIC GATAN (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 64

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 12761 / Applied symmetry: D8 (2*8 fold dihedral)
3D reconstructionAlgorithm: projection matching / Software: EMAN / CTF correction: Each CCD image / Resolution: 8 A / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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