[English] 日本語
Yorodumi
- EMDB-49054: Cryo-ET of FIB-milled synapse region between CD19+ NALM6 leukemia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49054
TitleCryo-ET of FIB-milled synapse region between CD19+ NALM6 leukemia cells and T-cells expressing 8H8 CD19 CAR construct, (sample 1).
Map dataLamella16_Position8, sample1
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: 4.61 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

-
Structure visualization

Supplemental images

emd_49054.png

Downloads & links

-
Map

FileDownload / File: emd_49054.map.gz / Format: CCP4 / Size: 11.6 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationLamella16_Position8, sample1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.61 Å/pix.
x 817 pix.
= 3767.187 Å		4.61 Å/pix.
x 3783 pix.
= 17443.414 Å		4.61 Å/pix.
x 4039 pix.
= 18623.83 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: 4.611 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-1.2264894 (±27.79637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin14433-396
Dimensions37834039817
Spacing40393783817
CellA: 18623.83 Å / B: 17443.414 Å / C: 3767.187 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
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.

-
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
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
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 {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
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: 49 / Average electron dose: 1.5 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: 26000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.61 Å / Software - Name: IMOD (ver. 4.11.25) / Number images used: 21
CTF correctionSoftware - Name: CTFFIND / Type: NONE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more