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- EMDB-39950: Cryo-EM structure of the gdTCR-ECD -

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Basic information

Entry
Database: EMDB / ID: EMD-39950
TitleCryo-EM structure of the gdTCR-ECD
Map data
Sample
  • Complex: TCR-CD3
    • Protein or peptide: TRA@ protein
    • Protein or peptide: gamma chain
Keywordscomplex / immune / 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: 2.9 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: Cryo-EM structure of the gdTCR-ECD
Authors: Bai Y / Zhu Y / Huang Z
History
DepositionMay 1, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39950.png

Downloads & links

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Map

FileDownload / File: emd_39950.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 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: 0.45
Minimum - Maximum-5.338356 - 8.274853
Average (Standard dev.)-0.0024834792 (±0.10621506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39950_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39950_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 : TCR-CD3

EntireName: TCR-CD3
Components
  • Complex: TCR-CD3
    • Protein or peptide: TRA@ protein
    • Protein or peptide: gamma chain

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Supramolecule #1: TCR-CD3

SupramoleculeName: TCR-CD3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1535676
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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