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- PDB-3j3x: Independent reconstruction of Mm-cpn cryo-EM density map from hal... -

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Basic information

Entry
Database: PDB / ID: 3j3x
TitleIndependent reconstruction of Mm-cpn cryo-EM density map from half dataset in the closed state (training map)
ComponentsChaperonin
KeywordsCHAPERONE / modeling / 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
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_database_related / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_database_related.content_type

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
E: Chaperonin
F: Chaperonin
G: Chaperonin
H: Chaperonin
I: Chaperonin
J: Chaperonin
K: Chaperonin
L: Chaperonin
M: Chaperonin
N: Chaperonin
O: Chaperonin
P: Chaperonin


Theoretical massNumber of molelcules
Total (without water)915,38916
Polymers915,38916
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Chaperonin /


Mass: 57211.828 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q877G8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mm-cpn with 1mM ATP/AlFx / Type: COMPLEX / Details: 16-mer
Molecular weightValue: 0.96 MDa / Experimental value: NO
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %
Details: Blotted once for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK III)
Method: 1 blot 3 seconds

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Feb 29, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 80000 X / Calibrated magnification: 112000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 4.1 mm
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
Camera length: 0 mm
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Specimen holder type: side-entry / Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter upper: 10 eV / Energyfilter lower: 0 eV
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: EMAN / Category: 3D reconstruction
CTF correctionDetails: Each micrograph
SymmetryPoint symmetry: D8 (2x8 fold dihedral)
3D reconstructionMethod: Projection matching / Resolution: 4.3 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 22571 / Nominal pixel size: 1.3 Å / Actual pixel size: 1.3 Å / Details: (Single particle--Applied symmetry: D8) / Symmetry type: POINT
Atomic model buildingPDB-ID: 1Q3Q

1q3q


Accession code: 1Q3Q / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms61264 0 0 0 61264

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