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- EMDB-17629: Symmetry expanded D7 local refined map of mitochondrial heat-shoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-17629
TitleSymmetry expanded D7 local refined map of mitochondrial heat-shock protein 60-like protein from Chaetomium thermophilum
Map data
Sample
  • Organelle or cellular component: native cell extract of Chaetomium thermophilum
    • Protein or peptide: Mitochondrial heat shock protein 60-like protein
Keywordsmitochondrial heat-shock protein 60-like protein / Stress response / ATP-binding / Nucleotide-binding / Chaetomium thermophilum / native cell extracts / CHAPERONE
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP binding
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / 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
Mitochondrial heat shock protein 60-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsSemchonok DA / Kyrilis FL / Hamdi F / Kastritis PL
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Symmetry expanded D7, locally refined cryo-EM map of mitochondrial heat shock protein 60-like protein Chaetomium thermophilum.
Authors: Semchonok DA / Kyrilis FL / Hamdi F / Kastritis PL
History
DepositionJun 13, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17629.png

Downloads & links

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Map

FileDownload / File: emd_17629.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.96 Å
Density
Contour LevelBy AUTHOR: 0.338
Minimum - Maximum-1.2281177 - 2.3216996
Average (Standard dev.)0.009488611 (±0.11615011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17629_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17629_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17629_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : native cell extract of Chaetomium thermophilum

EntireName: native cell extract of Chaetomium thermophilum
Components
  • Organelle or cellular component: native cell extract of Chaetomium thermophilum
    • Protein or peptide: Mitochondrial heat shock protein 60-like protein

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Supramolecule #1: native cell extract of Chaetomium thermophilum

SupramoleculeName: native cell extract of Chaetomium thermophilum / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Purified and fractionated (fraction 25) cell lysate of Chaetomium thermophilum
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 60 KDa

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Macromolecule #1: Mitochondrial heat shock protein 60-like protein

MacromoleculeName: Mitochondrial heat shock protein 60-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 60.669473 KDa
SequenceString: MQRALTRASV SSPLATARVR SAQQLRFAHK ELKFGVEGRA ALLNGVETLA KAVATTLGPK GRNVLIESTF GSPKITKDGV TVAKAISLK DKFENLGAKL LAEVASKTNE VAGDGTTTAT VLARAIFSEM VKNVAAGCNP MDLRRGIQAA VDAVVEYLQQ N KRDITTSA ...String:
MQRALTRASV SSPLATARVR SAQQLRFAHK ELKFGVEGRA ALLNGVETLA KAVATTLGPK GRNVLIESTF GSPKITKDGV TVAKAISLK DKFENLGAKL LAEVASKTNE VAGDGTTTAT VLARAIFSEM VKNVAAGCNP MDLRRGIQAA VDAVVEYLQQ N KRDITTSA EIAQVATISA NGDQHIGKLI ASAMEKVGKE GVITVKEGKT LQDELEVTEG MRFDRGFVSP YFITDAKAQK VE FEKPLIL LSEQKISAAT DIIPALEISH KMRRPLVIIA EDIDGEALAV CILNKLRGQL EVAAVKAPGF GDNRKSILGD IAV LTNGTV FTNELDVKLE KVTPDMLGST GSITITKEDT IILNGDGSKD AIAQRCEQIR GAMNDPSTSE YEKEKLQERL AKLS GGVAV IKVGGSSEVE VGEKKDRFVD ALNATRAAVE EGILPGGGTA LIKASVNALN NLKPANFDQQ LGVNIIKNAI TRPAR MIVE NAGLEGSVVI GKISDEYAAD FNKGFNSATG EYVDMIQAGI LDPLKVVRTG LIDASGVASL LGTTEVAIVE APEEKG PAG GMGGMGGMGG MM

UniProtKB: Mitochondrial heat shock protein 60-like protein

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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

Concentration0.3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1109 / Average electron dose: 28.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 287314
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 15942
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

ryb3


Chain - Chain ID: A / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Details: The initial model consisted of the complete monomeric unit of HSP60
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8pe8:
Symmetry expanded D7 local refined map of mitochondrial heat-shock protein 60-like protein from Chaetomium thermophilum

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