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- EMDB-63359: Structure of the gdTCR-Fab complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63359
TitleStructure of the gdTCR-Fab complex
Map data
Sample
  • Complex: Structure of the gdTCR-Fab complex
    • Protein or peptide: TRA@ protein
    • Protein or peptide: gamma chain
    • Protein or peptide: Light chain
    • Protein or peptide: Heavy chain
Keywordscomplex / Fab / gdTCR / IMMUNE SYSTEM
Function / homology
Function and homology information


T cell receptor complex / adaptive immune response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsBai Y / Zhu Y / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the gdTCR-Fab complex
Authors: Bai Y / Zhu Y / Huang Z
History
DepositionFeb 5, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63359.png

Downloads & links

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Map

FileDownload / File: emd_63359.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.1168478 - 9.328053000000001
Average (Standard dev.)-0.000038507165 (±0.025992533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63359_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63359_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the gdTCR-Fab complex

EntireName: Structure of the gdTCR-Fab complex
Components
  • Complex: Structure of the gdTCR-Fab complex
    • Protein or peptide: TRA@ protein
    • Protein or peptide: gamma chain
    • Protein or peptide: Light chain
    • Protein or peptide: Heavy chain

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Supramolecule #1: Structure of the gdTCR-Fab complex

SupramoleculeName: Structure of the gdTCR-Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TRA@ protein

MacromoleculeName: TRA@ protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.652867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QKVTQAQSSV SMPVRKAVTL NCLYETSWWS YYIFWYKQLP SKEMIFLIRQ GSDEQNAKSG RYSVNFKKAA KSVALTISAL QLEDSAKYF CALGDPGGLN TDKLIFGKGT RVTVEPRSQP HTKPSVFVMK NGTNVACLVK EFYPKDIRIN LVSSKKITEF D PAIVISPS ...String:
QKVTQAQSSV SMPVRKAVTL NCLYETSWWS YYIFWYKQLP SKEMIFLIRQ GSDEQNAKSG RYSVNFKKAA KSVALTISAL QLEDSAKYF CALGDPGGLN TDKLIFGKGT RVTVEPRSQP HTKPSVFVMK NGTNVACLVK EFYPKDIRIN LVSSKKITEF D PAIVISPS GKYNAVKLGK YEDSNSVTCS VQHDNKTVHS TDFE

UniProtKB: TRA@ protein, TRA@ protein

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Macromolecule #2: gamma chain

MacromoleculeName: gamma chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.888461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GTKSVTRPTR SSAEITCDLT VINAFYIHWY LHQEGKAPQR LLYYDVSNSK DVLESGLSPG KYYTHTPRRW SWILILRNLI ENDSGVYYC ATWDRGNPKT HYYKKLFGSG TTLVVTDKQL DADVSPKPTI FLPSIAETKL QKAGTYLCLL EKFFPDVIKI H WQEKKSNT ...String:
GTKSVTRPTR SSAEITCDLT VINAFYIHWY LHQEGKAPQR LLYYDVSNSK DVLESGLSPG KYYTHTPRRW SWILILRNLI ENDSGVYYC ATWDRGNPKT HYYKKLFGSG TTLVVTDKQL DADVSPKPTI FLPSIAETKL QKAGTYLCLL EKFFPDVIKI H WQEKKSNT ILGSQEGNTM KTNDTYMKFS WLTVPEESLD KEHRCIVRHE NNKNGVDQEI IFPPIK

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Macromolecule #3: Light chain

MacromoleculeName: Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.745951 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQTTSS LSASLGDRVT ISCRASQDIS NYLNWHQQKP DGTVKLLIYY TSRLHSGVPS RFSGSGSGTD YSLTISSLEQ EDIATYFCQ QSNTLPFTFG SGAKLEIK

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Macromolecule #4: Heavy chain

MacromoleculeName: Heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.687278 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SQVQLKESGP GLVAPSQSLS ITCTVSGFSL TSYGVHWVRQ PPGKGLEWLG VIWAGGNTDY NSALMSRLSI SKDNSKSRVF LKMNSLQTD DTAMYYCARE TTASFAYWGR GTLVTVSA

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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: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI MORGAGNI
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 187804
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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