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- EMDB-70748: Rabbit muscle aldolase from mixed sample prepared with Mix-it-up -

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Basic information

Entry
Database: EMDB / ID: EMD-70748
TitleRabbit muscle aldolase from mixed sample prepared with Mix-it-up
Map dataSharpened
Sample
  • Complex: Rabbit muscle aldolase
    • Protein or peptide: Rabbit muscle aldolase
Keywordsaldolase / lyase
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsAlexandrescu L / Lander GC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1F31NS136003-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM154216 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143805 United States
CitationJournal: To Be Published
Title: "Mix-it-up": Accessible time-resolved cryo-EM on the millisecond timescale
Authors: Alexandrescu L / Lander GC
History
DepositionMay 20, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70748.png

Downloads & links

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Map

FileDownload / File: emd_70748.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 200 pix.
= 188. Å		0.94 Å/pix.
x 200 pix.
= 188. Å		0.94 Å/pix.
x 200 pix.
= 188. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-2.028838 - 2.460906
Average (Standard dev.)0.0002462091 (±0.07686887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 188.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70748_msk_1.map
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AxesZYX

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Additional map: Unsharpened

Fileemd_70748_additional_1.map
AnnotationUnsharpened
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Half map: #2

Fileemd_70748_half_map_1.map
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Half map: #1

Fileemd_70748_half_map_2.map
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Sample components

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Entire : Rabbit muscle aldolase

EntireName: Rabbit muscle aldolase
Components
  • Complex: Rabbit muscle aldolase
    • Protein or peptide: Rabbit muscle aldolase

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Supramolecule #1: Rabbit muscle aldolase

SupramoleculeName: Rabbit muscle aldolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Lypholized
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 149.04 KDa

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Macromolecule #1: Rabbit muscle aldolase

MacromoleculeName: Rabbit muscle aldolase / type: protein_or_peptide / ID: 1 / Details: Fructose-bisphosphate aldolase / Enantiomer: LEVO / EC number: fructose-bisphosphate aldolase
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
SequenceString: HSHPALTPEQ KKELSDIAHR IVAPGKGILA ADESTGSIAK RLQSIGTENT EENRRFYRQL LLTADDRVNP CIGGVILFHE TLYQKADDGR PFPQVIKSKG GVVGIKVDKG VVPLAGTNGE TTTQGLDGLS ERCAQYKKDG ADFAKWRCVL KIGEHTPSAL AIMENANVLA ...String:
HSHPALTPEQ KKELSDIAHR IVAPGKGILA ADESTGSIAK RLQSIGTENT EENRRFYRQL LLTADDRVNP CIGGVILFHE TLYQKADDGR PFPQVIKSKG GVVGIKVDKG VVPLAGTNGE TTTQGLDGLS ERCAQYKKDG ADFAKWRCVL KIGEHTPSAL AIMENANVLA RYASICQQNG IVPIVEPEIL PDGDHDLKRC QYVTEKVLAA VYKALSDHHI YLEGTLLKPN MVTPGHACTQ KYSHEEIAMA TVTALRRTVP PAVTGVTFLS GGQSEEEASI NLNAINKCPL LKPWALTFSY GRALQASALK AWGGKKENLK AAQEEYVKRA LANSLACQGK YTP

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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

Concentration1.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
50.0 mMNaClSodium chloride
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 35 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 14 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 23.998 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 68 % / Chamber temperature: 296 K
Details: Vitrification at room temperature, ambient humidity, using specialized electrospray device, "Mix-it-Up".

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 70.0 K / Max: 77.0 K
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1673 / Average exposure time: 4.22 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: 3.483 µm / Calibrated defocus min: 0.1 µm / Calibrated magnification: 148936 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1185327
CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.2) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 185420
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
Final 3D classificationNumber classes: 50 / Avg.num./class: 14712 / Software - Name: cryoSPARC (ver. v4.6.2)
FSC plot (resolution estimation)

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