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- EMDB-49051: Cryo-ET of FIB-milled synapse region between CD19+ NALM6 leukemia... -

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Basic information

Entry
Database: EMDB / ID: EMD-49051
TitleCryo-ET of FIB-milled synapse region between CD19+ NALM6 leukemia cells and T-cells expressing 8H8 CD19 CAR construct, (sample2, region3).
Map dataLamella14_Position2, sample2 and region3
Sample
  • Cell: cryo-FIB milled synapse between CD19+ NALM6 leukemia cells and T-cells expressing 8H8 CD19 CAR construct.
KeywordsCAR T-cells / Hinge design / Immune Synapse / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 1.91 Å
AuthorsChen X / Walters KJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)ZIA BC 011627 United States
CitationJournal: To Be Published
Title: CAR-BOOSTing T-Cell Responsiveness through Synaptic Cleft Engineering
Authors: Mirazee J / Aranganathan A / Chen X / Tiwary P / Ding J / Mizuno N / Walters KJ / Taylor N / Gregoire AB
History
DepositionFeb 5, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49051.png

Downloads & links

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Map

FileDownload / File: emd_49051.map.gz / Format: CCP4 / Size: 3.8 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationLamella14_Position2, sample2 and region3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.91 Å/pix.
x 300 pix.
= 572.7 Å		1.91 Å/pix.
x 3531 pix.
= 6740.679 Å		1.91 Å/pix.
x 3897 pix.
= 7439.373 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.909 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-2.6448214 (±27.677676999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin28899-150
Dimensions35313897300
Spacing38973531300
CellA: 7439.373 Å / B: 6740.679 Å / C: 572.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : cryo-FIB milled synapse between CD19+ NALM6 leukemia cells and T-...

EntireName: cryo-FIB milled synapse between CD19+ NALM6 leukemia cells and T-cells expressing 8H8 CD19 CAR construct.
Components
  • Cell: cryo-FIB milled synapse between CD19+ NALM6 leukemia cells and T-cells expressing 8H8 CD19 CAR construct.

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Supramolecule #1: cryo-FIB milled synapse between CD19+ NALM6 leukemia cells and T-...

SupramoleculeName: cryo-FIB milled synapse between CD19+ NALM6 leukemia cells and T-cells expressing 8H8 CD19 CAR construct.
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
Details: RPMI (Thermo Fisher Scientific) supplemented with 8.9% FBS, Glutamax, and penicillin/streptomycin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 303 K / Instrument: LEICA EM GP
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 3600 / Focused ion beam - Temperature: 80 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2 FIB-SEM. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 33 / Average electron dose: 2.94 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: 5.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 64000
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

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.91 Å / Software - Name: IMOD (ver. 4.11.25) / Number images used: 25
CTF correctionSoftware - Name: CTFFIND / Type: NONE

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