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- EMDB-52284: Soft-landed and rehydrated GroEL -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52284
TitleSoft-landed and rehydrated GroEL
Map dataMap of soft-landed and rehydrated GroEL
Sample
  • Complex: groEL
    • Protein or peptide: GroEL
KeywordsChaperone
Function / homology
Function and homology information


coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity / positive regulation of T cell mediated immune response to tumor cell / chaperonin ATPase / Mitochondrial protein import / positive regulation of macrophage activation / negative regulation of execution phase of apoptosis / cellular response to interleukin-7 / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / biological process involved in interaction with symbiont / sperm plasma membrane / apoptotic mitochondrial changes / B cell activation / B cell proliferation / positive regulation of interferon-alpha production / DNA replication origin binding / positive regulation of interleukin-10 production / apolipoprotein binding / positive regulation of execution phase of apoptosis / response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / isomerase activity / chaperone-mediated protein complex assembly / sperm midpiece / clathrin-coated pit / positive regulation of interleukin-12 production / Mitochondrial protein degradation / response to cold / secretory granule / T cell activation / protein maturation / ATP-dependent protein folding chaperone / lipopolysaccharide binding / positive regulation of T cell activation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / p53 binding / unfolded protein binding / protein folding / single-stranded DNA binding / double-stranded RNA binding / protein-folding chaperone binding / protein refolding / early endosome / mitochondrial inner membrane / protein stabilization / mitochondrial matrix / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
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
60 kDa heat shock protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / Resolution: 3.9 Å
AuthorsBarrass SV / Esser TK / Mowry NJ / Eriksson L / Hruby J / Seeley LT / Drabbels M / Baker LA / Rauschenbach S / Lorenz UJ
Funding support Switzerland, United Kingdom, European Union, 6 items
OrganizationGrant numberCountry
Swiss National Science Foundation213773 Switzerland
Swiss National Science Foundation207842 Switzerland
UK Research and Innovation (UKRI)EP/V051474/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V019694/1 United Kingdom
H2020 Marie Curie Actions of the European Commission883387European Union
Wellcome Trust218482/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM Sample Preparation Using Soft-landing Electrospray Ion Beam Deposition and Laser Flash Melting
Authors: Barrass SV / Esser TK / Mowry NJ / Eriksson L / Hruby J / Seeley LT / Drabbels M / Baker LA / Rauschenbach S / Lorenz UJ
History
DepositionDec 6, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52284.png

Downloads & links

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Map

FileDownload / File: emd_52284.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of soft-landed and rehydrated GroEL
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 256 pix.
= 371.712 Å		1.45 Å/pix.
x 256 pix.
= 371.712 Å		1.45 Å/pix.
x 256 pix.
= 371.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.452 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0569
Minimum - Maximum-0.11971412 - 0.39351842
Average (Standard dev.)0.0017515176 (±0.014751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 371.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of soft-landed and rehydrated GroEL

Fileemd_52284_half_map_1.map
AnnotationHalf map A of soft-landed and rehydrated GroEL
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of soft-landed and rehydrated GroEL

Fileemd_52284_half_map_2.map
AnnotationHalf map B of soft-landed and rehydrated GroEL
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : groEL

EntireName: groEL
Components
  • Complex: groEL
    • Protein or peptide: GroEL

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Supramolecule #1: groEL

SupramoleculeName: groEL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MLRLPTVFRQ MRPVSRVLAP HLTRAYAKDV KFGADARALM LQGVDLLADA VAVTMGPKGR TVIIEQSWG SPKVTKDGVT VAKSIDLKDK YKNIGAKLVQ DVANNTNEEA GDGTTTATVL A RSIAKEGF EKISKGANPV EIRRGVMLAV DAVIAELKKQ SKPVTTPEEI ...String:
MLRLPTVFRQ MRPVSRVLAP HLTRAYAKDV KFGADARALM LQGVDLLADA VAVTMGPKGR TVIIEQSWG SPKVTKDGVT VAKSIDLKDK YKNIGAKLVQ DVANNTNEEA GDGTTTATVL A RSIAKEGF EKISKGANPV EIRRGVMLAV DAVIAELKKQ SKPVTTPEEI AQVATISANG DK EIGNIIS DAMKKVGRKG VITVKDGKTL NDELEIIEGM KFDRGYISPY FINTSKGQKC EFQ DAYVLL SEKKISSIQS IVPALEIANA HRKPLVIIAE DVDGEALSTL VLNRLKVGLQ VVAV KAPGF GDNRKNQLKD MAIATGGAVF GEEGLTLNLE DVQPHDLGKV GEVIVTKDDA MLLKG KGDK AQIEKRIQEI IEQLDVTTSE YEKEKLNERL AKLSDGVAVL KVGGTSDVEV NEKKDR VTD ALNATRAAVE EGIVLGGGCA LLRCIPALDS LTPANEDQKI GIEIIKRTLK IPAMTIA KN AGVEGSLIVE KIMQSSSEVG YDAMAGDFVN MVEKGIIDPT KVVRTALLDA AGVASLLT T AEVVVTEIPK EEKDPGMGAM GGMGGGMGGG MF

UniProtKB: 60 kDa heat shock protein, mitochondrial

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
DetailsGroEL was deposited onto a cryo-EM grid using soft-landing electrospray ion beam deposition. 50 nm of amorphous ice was deposited onto the sample and laser flash melting and revitrification was used to rehydrate the protein.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 44000 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3455984
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Software - details: Non-uniform refinement / Number images used: 119637
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5) / Software - details: ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD

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