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- EMDB-72177: Dihydroneopterin aldolase encapsulated in an MS2-nanocrate: MS2nc@DHNA -

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Basic information

Entry
Database: EMDB / ID: EMD-72177
TitleDihydroneopterin aldolase encapsulated in an MS2-nanocrate: MS2nc@DHNA
Map datasharpened
Sample
  • Complex: Dihydroneopterin aldolase
KeywordsDHNA / nanocrate / lyase
Biological speciesYersinia pestis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsKopylov M / Bobe D / Jenkins MC / Bourne CR / Zimanyi CM
Funding support United States, 3 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI148382 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA247484 United States
CitationJournal: To Be Published
Title: Overcoming air-water interface-induced artifacts in Cryo-EM with protein nanocrates
Authors: Jenkins MC / Bobe D / Johnston JD / Cheung J / Karasawa A / Zimanyi CM / Dermanci O / Finn MG / de Marco A / Kopylov M
History
DepositionAug 15, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72177.png

Downloads & links

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Map

FileDownload / File: emd_72177.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 396.48 Å		0.83 Å/pix.
x 480 pix.
= 396.48 Å		0.83 Å/pix.
x 480 pix.
= 396.48 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.611
Minimum - Maximum-1.8777434 - 3.1729689
Average (Standard dev.)0.0054238895 (±0.044259883)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 396.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72177_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: unsharpened

Fileemd_72177_additional_1.map
Annotationunsharpened
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: halfA

Fileemd_72177_half_map_1.map
AnnotationhalfA
Projections & Slices
AxesZYX

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Histogram

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Half map: halfB

Fileemd_72177_half_map_2.map
AnnotationhalfB
Projections & Slices
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Sample components

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Entire : Dihydroneopterin aldolase

EntireName: Dihydroneopterin aldolase
Components
  • Complex: Dihydroneopterin aldolase

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Supramolecule #1: Dihydroneopterin aldolase

SupramoleculeName: Dihydroneopterin aldolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Recombinantly expressed Dihydroneopterin aldolase from Yersinia pestis
Source (natural)Organism: Yersinia pestis (bacteria)

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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

BufferpH: 8.5 / Details: 100 mM Tris-HCl [pH 8.5], 80 mM KCl, 10 mM MgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2860 / Average exposure time: 1.25 sec. / Average electron dose: 54.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 112060
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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