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- EMDB-10884: HSPD1 single ring deposited by spraying (50 ms delay) -

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Basic information

Entry
Database: EMDB / ID: EMD-10884
TitleHSPD1 single ring deposited by spraying (50 ms delay)
Map dataunsharpened final map
Sample
  • Complex: human mitochondrial 60 kDa heat shock protein (mature)
    • Protein or peptide: human mitochondrial 60 kDa heat shock protein (mature)
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 / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell ...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 / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / Mitochondrial protein import / chaperonin ATPase / positive regulation of macrophage activation / cellular response to interleukin-7 / biological process involved in interaction with symbiont / MyD88-dependent toll-like receptor signaling pathway / sperm plasma membrane / 'de novo' protein folding / B cell proliferation / DNA replication origin binding / apolipoprotein binding / B cell activation / positive regulation of interferon-alpha production / protein maturation / apoptotic mitochondrial changes / positive regulation of interleukin-10 production / response to unfolded protein / chaperone-mediated protein complex assembly / clathrin-coated pit / sperm midpiece / Mitochondrial protein degradation / positive regulation of interleukin-12 production / response to cold / T cell activation / secretory granule / isomerase activity / lipopolysaccharide binding / ATP-dependent protein folding chaperone / : / positive regulation of interleukin-6 production / positive regulation of type II interferon production / double-stranded RNA binding / positive regulation of T cell activation / unfolded protein binding / p53 binding / protein folding / protein-folding chaperone binding / single-stranded DNA binding / protein refolding / mitochondrial inner membrane / early endosome / protein stabilization / mitochondrial matrix / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / 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 / cryo EM / Resolution: 6.8 Å
AuthorsKlebl DP / Gravett MSC / Darrow M / Thompson RF / Muench SP
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P020208/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P026397/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: Structure / Year: 2020
Title: Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales.
Authors: David P Klebl / Molly S C Gravett / Dimitrios Kontziampasis / David J Wright / Robin S Bon / Diana C F Monteiro / Martin Trebbin / Frank Sobott / Howard D White / Michele C Darrow / Rebecca ...Authors: David P Klebl / Molly S C Gravett / Dimitrios Kontziampasis / David J Wright / Robin S Bon / Diana C F Monteiro / Martin Trebbin / Frank Sobott / Howard D White / Michele C Darrow / Rebecca F Thompson / Stephen P Muench /
Abstract: A host of new technologies are under development to improve the quality and reproducibility of cryoelectron microscopy (cryoEM) grid preparation. Here we have systematically investigated the ...A host of new technologies are under development to improve the quality and reproducibility of cryoelectron microscopy (cryoEM) grid preparation. Here we have systematically investigated the preparation of three macromolecular complexes using three different vitrification devices (Vitrobot, chameleon, and a time-resolved cryoEM device) on various timescales, including grids made within 6 ms (the fastest reported to date), to interrogate particle behavior at the air-water interface for different timepoints. Results demonstrate that different macromolecular complexes can respond to the thin-film environment formed during cryoEM sample preparation in highly variable ways, shedding light on why cryoEM sample preparation can be difficult to optimize. We demonstrate that reducing time between sample application and vitrification is just one tool to improve cryoEM grid quality, but that it is unlikely to be a generic "silver bullet" for improving the quality of every cryoEM sample preparation.
History
DepositionApr 17, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.083
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.083
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10884.png

Downloads & links

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Map

FileDownload / File: emd_10884.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened final map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 124 pix.
= 264.12 Å		2.13 Å/pix.
x 124 pix.
= 264.12 Å		2.13 Å/pix.
x 124 pix.
= 264.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.083 / Movie #1: 0.083
Minimum - Maximum-0.08343847 - 0.25357452
Average (Standard dev.)0.00014410625 (±0.015647853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions124124124
Spacing124124124
CellA=B=C: 264.12003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.132.132.13
M x/y/z124124124
origin x/y/z0.0000.0000.000
length x/y/z264.120264.120264.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS124124124
D min/max/mean-0.0830.2540.000

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Supplemental data

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Mask #1

Fileemd_10884_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10884_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10884_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 : human mitochondrial 60 kDa heat shock protein (mature)

EntireName: human mitochondrial 60 kDa heat shock protein (mature)
Components
  • Complex: human mitochondrial 60 kDa heat shock protein (mature)
    • Protein or peptide: human mitochondrial 60 kDa heat shock protein (mature)

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Supramolecule #1: human mitochondrial 60 kDa heat shock protein (mature)

SupramoleculeName: human mitochondrial 60 kDa heat shock protein (mature)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: human mitochondrial 60 kDa heat shock protein (mature)

MacromoleculeName: human mitochondrial 60 kDa heat shock protein (mature)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAAKDVKFG ADARALMLQG VDLLADAVAV TMGPKGRTVI IEQSWGSPKV TKDGVTVAKS IDLKDKYKNI GAKLVQDVAN NTNEEAGDGT TTATVLARSI AKEGFEKISK GANPVEIRRG VMLAVDAVIA ELKKQSKPVT TPEEIAQVAT ISANGDKEIG NIISDAMKKV ...String:
SNAAKDVKFG ADARALMLQG VDLLADAVAV TMGPKGRTVI IEQSWGSPKV TKDGVTVAKS IDLKDKYKNI GAKLVQDVAN NTNEEAGDGT TTATVLARSI AKEGFEKISK GANPVEIRRG VMLAVDAVIA ELKKQSKPVT TPEEIAQVAT ISANGDKEIG NIISDAMKKV GRKGVITVKD GKTLNDELEI IEGMKFDRGY ISPYFINTSK GQKCEFQDAY VLLSEKKISS IQSIVPALEI ANAHRKPLVI IAEDVDGEAL STLVLNRLKV GLQVVAVKAP GFGDNRKNQL KDMAIATGGA VFGEEGLTLN LEDVQPHDLG KVGEVIVTKD DAMLLKGKGD KAQIEKRIQE IIEQLDVTTS EYEKEKLNER LAKLSDGVAV LKVGGTSDVE VNEKKDRVTD ALNATRAAVE EGIVLGGGCA LLRCIPALDS LTPANEDQKI GIEIIKRTLK IPAMTIAKNA GVEGSLIVEK IMQSSSEVGY DAMAGDFVNM VEKGIIDPTK VVRTALLDAA GVASLLTTAE VVVTEIPKEE KDPGMGAMGG MGGGMGGGMF

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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

Concentration4.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293 K / Instrument: HOMEMADE PLUNGER
Details: the sample was sprayed using a microfludic nozzle, resulting in a delay of 50ms between spraying and freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.5 sec. / Average electron dose: 81.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 39610
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Details: The final angular assignment was done in a bigger, combined dataset which was then split into the original datasets to generate this reconstruction
FSC plot (resolution estimation)

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