[English] 日本語
Yorodumi
- EMDB-52605: 3D reconstruction of Themis:Grb2:ProMacrobody256 after 3D classif... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52605
Title3D reconstruction of Themis:Grb2:ProMacrobody256 after 3D classification (Class 2)
Map dataSharpened map of 3D reconstruction of the Themis:Grb2:ProMacrobody256 complex after 3D classification (Class 2)
Sample
  • Complex: Themis-Grb2 complex bound to ProMacrobody 256
    • Protein or peptide: Grb2
    • Protein or peptide: Themis (1-563)
    • Protein or peptide: ProMacrobody 256
Keywordsadapter protein / CABIT / TCR / T cell development / SIGNALING PROTEIN
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsClancy DM / Felix J / Bloch Y / Savvides SN
Funding support Belgium, 2 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1219923N Belgium
Research Foundation - Flanders (FWO)G049820N Belgium
CitationJournal: Nat Commun / Year: 2026
Title: Structural and mechanistic insights into the constitutive Themis-Grb2 complex in T cell signalling.
Authors: Danielle M Clancy / Alba Sanz-Sanjuan / Elisabeth Gilis / Peter Tougaard / Imke Velghe / Yana Van Droogenbroeck / Jan Felix / Yehudi Bloch / Álvaro Furones Cuadrado / Romain Merceron / ...Authors: Danielle M Clancy / Alba Sanz-Sanjuan / Elisabeth Gilis / Peter Tougaard / Imke Velghe / Yana Van Droogenbroeck / Jan Felix / Yehudi Bloch / Álvaro Furones Cuadrado / Romain Merceron / Stephan Schenck / Peter Vandenabeele / Janine D Brunner / Tom Taghon / Dirk Elewaut / Savvas N Savvides /
Abstract: Thymocyte selection is essential for establishing the T cell repertoire, maintaining self-tolerance and preventing autoimmunity. Themis, the archetypal member of a metazoan protein family defined by ...Thymocyte selection is essential for establishing the T cell repertoire, maintaining self-tolerance and preventing autoimmunity. Themis, the archetypal member of a metazoan protein family defined by CABIT domains, centrally regulates this process by integrating T cell receptor (TCR) signalling. Themis has been proposed to constitutively partner with the multifunctional adaptor Grb2, yet the structural and mechanistic basis of this assembly has remained enigmatic. Here, we use Cryo-EM to reveal how the tandem CABIT domains and proline-rich sequence of Themis cooperatively engulf the C-terminal SH3 domain of Grb2, while the unbound domains of Grb2 remain poised to recruit additional binding partners. Furthermore, we uncover inherent interdomain flexibility in unbound Themis that resolves upon Grb2 binding. Structure-guided mutations abrogate the Themis-Grb2 interaction and fail to regulate the tyrosine phosphatase SHP-1 after TCR stimulation, recapitulating the phenotype of Themis-deficient cells. Our findings define the Themis-Grb2 complex as a dynamic structural hub in T cell signalling.
History
DepositionJan 23, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52605.png

Downloads & links

-
Map

FileDownload / File: emd_52605.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of 3D reconstruction of the Themis:Grb2:ProMacrobody256 complex after 3D classification (Class 2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 416 pix.
= 314.08 Å		0.76 Å/pix.
x 416 pix.
= 314.08 Å		0.76 Å/pix.
x 416 pix.
= 314.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.755 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.18657675 - 0.42538753
Average (Standard dev.)0.00032967466 (±0.0080518825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 314.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map 1 of 3D reconstruction of the...

Fileemd_52605_half_map_1.map
AnnotationHalf map 1 of 3D reconstruction of the Themis:Grb2:ProMacrobody256 complex after 3D classification (Class 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 of 3D reconstruction of the...

Fileemd_52605_half_map_2.map
AnnotationHalf map 2 of 3D reconstruction of the Themis:Grb2:ProMacrobody256 complex after 3D classification (Class 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Themis-Grb2 complex bound to ProMacrobody 256

EntireName: Themis-Grb2 complex bound to ProMacrobody 256
Components
  • Complex: Themis-Grb2 complex bound to ProMacrobody 256
    • Protein or peptide: Grb2
    • Protein or peptide: Themis (1-563)
    • Protein or peptide: ProMacrobody 256

-
Supramolecule #1: Themis-Grb2 complex bound to ProMacrobody 256

SupramoleculeName: Themis-Grb2 complex bound to ProMacrobody 256 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 142 KDa

-
Macromolecule #1: Grb2

MacromoleculeName: Grb2 / type: protein_or_peptide / ID: 1
Details: Human Growth factor-receptor bound protein 2 (Grb2) residues 1-217 with C-terminal His tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEAIAKYDFK ATADDELSFK RGDILKVLNE ECDQNWYKAE LNGKDGFIPK NYIEMKPHPW FFGKIPRAKA EEMLSKQRHD GAFLIRESES APGDFSLSVK FGNDVQHFKV LRDGAGKYFL WVVKFNSLNE LVDYHRSTSV SRNQQIFLRD IEQVPQQPTY VQALFDFDPQ ...String:
MEAIAKYDFK ATADDELSFK RGDILKVLNE ECDQNWYKAE LNGKDGFIPK NYIEMKPHPW FFGKIPRAKA EEMLSKQRHD GAFLIRESES APGDFSLSVK FGNDVQHFKV LRDGAGKYFL WVVKFNSLNE LVDYHRSTSV SRNQQIFLRD IEQVPQQPTY VQALFDFDPQ EDGELGFRRG DFIHVMDNSD PNWWKGACHG QTGMFPRNYV TPVNRNVKHH HHHH

-
Macromolecule #2: Themis (1-563)

MacromoleculeName: Themis (1-563) / type: protein_or_peptide / ID: 2 / Details: Human Themis residues 1-563 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALSLEEFVH SLDLRTLPRV LEIQAGIYLE GSIYEMFGNE CCFSTGEVIK ITGLKVKKII AEICEQIEGC ESLQPFELPM NFPGLFKIVA DKTPYLTMEE ITRTIHIGPS RLGHPCFYHQ KDIKLENLII KQGEQIMLNS VEEIDGEIMV SCAVARNHQT HSFNLPLSQE ...String:
MALSLEEFVH SLDLRTLPRV LEIQAGIYLE GSIYEMFGNE CCFSTGEVIK ITGLKVKKII AEICEQIEGC ESLQPFELPM NFPGLFKIVA DKTPYLTMEE ITRTIHIGPS RLGHPCFYHQ KDIKLENLII KQGEQIMLNS VEEIDGEIMV SCAVARNHQT HSFNLPLSQE GEFYECEDER IYTLKEIVEW KIPKNRTRTV NLTDFSNKWD STNPFPKDFY GTLILKPVYE IQGVMKFRKD IIRILPSLDV EVKDITDSYD ANWFLQLLST EDLFEMTSKE FPIVTEVIEA PEGNHLPQSI LQPGKTIVIH KKYQASRILA SEIRSNFPKR HFLIPTSYKG KFKRRPREFP TAYDLEIAKS EKEPLHVVAT KAFHSPHDKL SSVSVGDQFL VHQSETTEVL CEGIKKVVNV LACEKILKKS YEAALLPLYM EGGFVEVIHD KKQYPISELC KQFRLPFNVK VSVRDLSIEE DVLAATPGLQ LEEDITDSYL LISDFANPTE CWEIPVGRLN MTVQLVSNFS RDAEPFLVRT LVEEITEEQY YMMRRYESSA SHPPPRPPKH PSV

-
Macromolecule #3: ProMacrobody 256

MacromoleculeName: ProMacrobody 256 / type: protein_or_peptide / ID: 3
Details: ProMacrobody 256 (Themis-specific Nanobody 256 fused via rigid proline linker to MBP)
Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVQLQESGGG LVQAGGSLRL SCAASGRTFS TYAMGWFRQA PGKEREFVAA ILWSDGSTYY ADSVKGRFTI SRDNAKNTVY LQMNSLKPED TAVYYCAADY TGVRYDYWGQ GTQVTVPPLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD ...String:
QVQLQESGGG LVQAGGSLRL SCAASGRTFS TYAMGWFRQA PGKEREFVAA ILWSDGSTYY ADSVKGRFTI SRDNAKNTVY LQMNSLKPED TAVYYCAADY TGVRYDYWGQ GTQVTVPPLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW PLIAADGGYA FKYENGKYDI KDVGVDNAGA KAGLTFLVDL IKNKHMNADT DYSIAEAAFN KGETAMTING PWAWSNIDTS KVNYGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGAVALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKDAQT

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
25.0 mMTrisTris(hydroxymethyl)aminomethane
2.0 mMDTTDithiothreitol
8.0 mMCHAPSOCHAPSO

Details: 25 mM Tris pH8, 100 mM NaCl, 2 mM DTT with added 8 mM CHAPSO for cryogrid sample preparation
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP / Details: Leica EM GP2, 5 s blotting time.

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 27698 / Average exposure time: 3.37 sec. / Average electron dose: 61.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 60000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.1) / Number images used: 28445
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.5.1)
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC (ver. v4.5.1)
FSC plot (resolution estimation)

+
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