[English] 日本語
Yorodumi
- EMDB-61883: Fab-CD3-gamma epsilon-TCR complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61883
TitleFab-CD3-gamma epsilon-TCR complex
Map data
Sample
  • Complex: Fab-CD3-gamma epsilon-TCR complex
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: T cell receptor delta variable 2,T cell receptor delta constant
    • Protein or peptide: T cell receptor gamma variable 9,T cell receptor gamma constant 1
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain
  • Ligand: CHOLESTEROL
KeywordsT cell receptor / gamma delta TCR / immune cell / Fab complex / IMMUNE SYSTEM
Function / homology
Function and homology information


MHC protein binding / regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / positive regulation of cell-cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway / gamma-delta T cell activation ...MHC protein binding / regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / positive regulation of cell-cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / positive thymic T cell selection / signal complex assembly / positive regulation of protein localization to cell surface / Nef and signal transduction / alpha-beta T cell receptor complex / positive regulation of cell-matrix adhesion / T cell receptor complex / smoothened signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / small molecule binding / positive regulation of interleukin-4 production / dendrite development / establishment or maintenance of cell polarity / protein complex oligomerization / alpha-beta T cell activation / FCGR activation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / Role of phospholipids in phagocytosis / positive regulation of interleukin-2 production / T cell costimulation / T cell receptor binding / positive regulation of T cell proliferation / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / cerebellum development / protein tyrosine kinase binding / T cell activation / FCGR3A-mediated phagocytosis / negative regulation of smoothened signaling pathway / apoptotic signaling pathway / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / peptide antigen binding / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / T cell receptor signaling pathway / protein transport / Clathrin-mediated endocytosis / signaling receptor complex adaptor activity / cell body / protein-containing complex assembly / regulation of apoptotic process / dendritic spine / adaptive immune response / protein-macromolecule adaptor activity / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / protein heterodimerization activity / external side of plasma membrane / negative regulation of gene expression / innate immune response / positive regulation of gene expression / protein kinase binding / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / T-cell surface glycoprotein CD3 zeta subunit / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif ...: / : / T-cell surface glycoprotein CD3 zeta subunit / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T cell receptor delta variable 2 / T cell receptor delta constant / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 epsilon chain / T-cell surface glycoprotein CD3 gamma chain / T cell receptor gamma constant 1 / T-cell surface glycoprotein CD3 zeta chain / T cell receptor gamma variable 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsWang L / Li J / Li Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structures of the apo and agonist-crosslinked human gamma delta T-cell receptor
Authors: Wang L / Li Z / Fan Y / Li J
History
DepositionOct 12, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61883.png

Downloads & links

-
Map

FileDownload / File: emd_61883.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 421.888 Å		0.82 Å/pix.
x 512 pix.
= 421.888 Å		0.82 Å/pix.
x 512 pix.
= 421.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.687274 - 1.0856876
Average (Standard dev.)-0.00020720459 (±0.012853624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 421.888 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_61883_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61883_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Fab-CD3-gamma epsilon-TCR complex

EntireName: Fab-CD3-gamma epsilon-TCR complex
Components
  • Complex: Fab-CD3-gamma epsilon-TCR complex
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: T cell receptor delta variable 2,T cell receptor delta constant
    • Protein or peptide: T cell receptor gamma variable 9,T cell receptor gamma constant 1
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain
  • Ligand: CHOLESTEROL

+
Supramolecule #1: Fab-CD3-gamma epsilon-TCR complex

SupramoleculeName: Fab-CD3-gamma epsilon-TCR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: T-cell surface glycoprotein CD3 zeta chain

MacromoleculeName: T-cell surface glycoprotein CD3 zeta chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.881598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MKWKALFTAA ILQAQLPITE AQSFGLLDPK LCYLLDGILF IYGVILTALF LRVKFSRSAD APAYQQGQNQ LYNELNLGRR EEYDVLDKR RGRDPEMGGK PQRRKNPQEG LYNELQKDKM AEAYSEIGMK GERRRGKGHD GLYQGLSTAT KDTYDALHMQ A LPPRSA

UniProtKB: T-cell surface glycoprotein CD3 zeta chain

+
Macromolecule #2: T-cell surface glycoprotein CD3 delta chain

MacromoleculeName: T-cell surface glycoprotein CD3 delta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.949537 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEHSTFLSGL VLATLLSQVS PFKIPIEELE DRVFVNCNTS ITWVEGTVGT LLSDITRLDL GKRILDPRGI YRCNGTDIYK DKESTVQVH YRMCQSCVEL DPATVAGIIV TDVIATLLLA LGVFCFAGHE TGRLSGAADT QALLRNDQVY QPLRDRDDAQ Y SHLGGNWA RNK

UniProtKB: T-cell surface glycoprotein CD3 delta chain

+
Macromolecule #3: T-cell surface glycoprotein CD3 epsilon chain

MacromoleculeName: T-cell surface glycoprotein CD3 epsilon chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.174227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQSGTHWRVL GLCLLSVGVW GQDGNEEMGG ITQTPYKVSI SGTTVILTCP QYPGSEILWQ HNDKNIGGDE DDKNIGSDED HLSLKEFSE LEQSGYYVCY PRGSKPEDAN FYLYLRARVC ENCMEMDVMS VATIVIVDIC ITGGLLLLVY YWSKNRKAKA K PVTRGAGA ...String:
MQSGTHWRVL GLCLLSVGVW GQDGNEEMGG ITQTPYKVSI SGTTVILTCP QYPGSEILWQ HNDKNIGGDE DDKNIGSDED HLSLKEFSE LEQSGYYVCY PRGSKPEDAN FYLYLRARVC ENCMEMDVMS VATIVIVDIC ITGGLLLLVY YWSKNRKAKA K PVTRGAGA GGRQRGQNKE RPPPVPNPDY EPIRKGQRDL YSGLNQRRI

UniProtKB: T-cell surface glycoprotein CD3 epsilon chain

+
Macromolecule #4: T cell receptor delta variable 2,T cell receptor delta constant

MacromoleculeName: T cell receptor delta variable 2,T cell receptor delta constant
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.662697 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQRISSLIHL SLFWAGVMSA IELVPEHQTV PVSIGVPATL RCSMKGEAIG NYYINWYRKT QGNTMTFIYR EKDIYGPGFK DNFQGDIDI AKNLAVLKIL APSERDEGSY YCACDTLGMG GEYTDKLIFG KGTRVTVEPR SQPHTKPSVF VMKNGTNVAC L VKEFYPKD ...String:
MQRISSLIHL SLFWAGVMSA IELVPEHQTV PVSIGVPATL RCSMKGEAIG NYYINWYRKT QGNTMTFIYR EKDIYGPGFK DNFQGDIDI AKNLAVLKIL APSERDEGSY YCACDTLGMG GEYTDKLIFG KGTRVTVEPR SQPHTKPSVF VMKNGTNVAC L VKEFYPKD IRINLVSSKK ITEFDPAIVI SPSGKYNAVK LGKYEDSNSV TCSVQHDNKT VHSTDFEVKT DSTDHVKPKE TE NTKQPSK SCHKPKAIVH TEKVNMMSLT VLGLRMLFAK TVAVNFLLTA KLFFL

UniProtKB: T cell receptor delta variable 2, T cell receptor delta constant

+
Macromolecule #5: T cell receptor gamma variable 9,T cell receptor gamma constant 1

MacromoleculeName: T cell receptor gamma variable 9,T cell receptor gamma constant 1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.395801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLSLLHTSTL AVLGALCVYG AGHLEQPQIS STKTLSKTAR LECVVSGITI SATSVYWYRE RPGEVIQFLV SISYDGTVRK ESGIPSGKF EVDRIPETST STLTIHNVEK QDIATYYCAL WEAQQELGKK IKVFGPGTKL IITDKQLDAD VSPKPTIFLP S IAETKLQK ...String:
MLSLLHTSTL AVLGALCVYG AGHLEQPQIS STKTLSKTAR LECVVSGITI SATSVYWYRE RPGEVIQFLV SISYDGTVRK ESGIPSGKF EVDRIPETST STLTIHNVEK QDIATYYCAL WEAQQELGKK IKVFGPGTKL IITDKQLDAD VSPKPTIFLP S IAETKLQK AGTYLCLLEK FFPDVIKIHW EEKKSNTILG SQEGNTMKTN DTYMKFSWLT VPEKSLDKEH RCIVRHENNK NG VDQEIIF PPIKTDVITM DPKDNCSKDA NDTLLLQLTN TSAYYMYLLL LLKSVVYFAI ITCCLLRRTA FCCNGEKS

UniProtKB: T cell receptor gamma variable 9, T cell receptor gamma constant 1

+
Macromolecule #6: T-cell surface glycoprotein CD3 gamma chain

MacromoleculeName: T-cell surface glycoprotein CD3 gamma chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.493457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEQGKGLAVL ILAIILLQGT LAQSIKGNHL VKVYDYQEDG SVLLTCDAEA KNITWFKDGK MIGFLTEDKK KWNLGSNAKD PRGMYQCKG SQNKSKPLQV YYRMCQNCIE LNAATISGFL FAEIVSIFVL AVGVYFIAGQ DGVRQSRASD KQTLLPNDQL Y QPLKDRED DQYSHLQGNQ LRRN

UniProtKB: T-cell surface glycoprotein CD3 gamma chain

+
Macromolecule #7: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.475863 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQTTSS LSASLGDRVT ISCRASQDIR NYLNWYQQKP DGTVKLLIYY TSRLHSGVPS KFSGSGSGTD YSLTISNLEQ EDIATYFCQ QGNTLPWTFA GGTKLEIKRA DAAPTVSIFP PASEQLTSGG ASVVCFLNNF YPKSINSKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQTTSS LSASLGDRVT ISCRASQDIR NYLNWYQQKP DGTVKLLIYY TSRLHSGVPS KFSGSGSGTD YSLTISNLEQ EDIATYFCQ QGNTLPWTFA GGTKLEIKRA DAAPTVSIFP PASEQLTSGG ASVVCFLNNF YPKSINSKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKNEYER HNSYTCEATH KTSTSPIVKS FNRS

+
Macromolecule #8: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.00298 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLQQSGPE LVKPGASMKI SCKASGYSFT GYTMNWVKQS HGKNLEWMGL INPYKGVSTY NQKFKDKATL TVDKSSSTAY MELLSLTSE DSAVYYCARS GYYGDSDWYF DVWGQGTTLT VFSAKTTPPS VYPLAPGSAA QTNSMVTLGC LVKGYFPEPV T VTWNSGSL ...String:
EVQLQQSGPE LVKPGASMKI SCKASGYSFT GYTMNWVKQS HGKNLEWMGL INPYKGVSTY NQKFKDKATL TVDKSSSTAY MELLSLTSE DSAVYYCARS GYYGDSDWYF DVWGQGTTLT VFSAKTTPPS VYPLAPGSAA QTNSMVTLGC LVKGYFPEPV T VTWNSGSL SSGVHTFPAV LKSDLYTLSS SVTVPSSPRP SETVTCNVAH PASSTTVDKK IVPR

+
Macromolecule #9: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 9 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9jxz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66602
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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