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- EMDB-60046: CryoEM structure of GR2002-F(ab')2: TSLP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60046
TitleCryoEM structure of GR2002-F(ab')2: TSLP complex
Map data
Sample
  • Complex: GR2002-F(ab')2: TSLP complex
    • Protein or peptide: Fab-H1A10 fragment, heavy chain
    • Protein or peptide: Fab fragment, light chain
    • Protein or peptide: Thymic stromal lymphopoietin
    • Protein or peptide: Fab-H3B10 fragment, heavy chain
KeywordsCryo-EM / TSLP-F(ab')2 complex / bispecific antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of chemokine (C-C motif) ligand 1 production / interleukin-7 receptor binding / positive regulation of granulocyte colony-stimulating factor production / positive regulation of mast cell activation / positive regulation of cytokine-mediated signaling pathway / positive regulation of receptor signaling pathway via STAT / interleukin-7-mediated signaling pathway / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / positive regulation of interleukin-10 production ...positive regulation of chemokine (C-C motif) ligand 1 production / interleukin-7 receptor binding / positive regulation of granulocyte colony-stimulating factor production / positive regulation of mast cell activation / positive regulation of cytokine-mediated signaling pathway / positive regulation of receptor signaling pathway via STAT / interleukin-7-mediated signaling pathway / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / positive regulation of interleukin-10 production / cell surface receptor signaling pathway via JAK-STAT / defense response to fungus / positive regulation of chemokine production / Interleukin-7 signaling / cytokine activity / positive regulation of interleukin-6 production / cytokine-mediated signaling pathway / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular region
Similarity search - Function
Thymic stromal lymphopoietin / Thymic stromal lymphopoietin superfamily / Thymic stromal lymphopoietin
Similarity search - Domain/homology
Thymic stromal lymphopoietin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsZhigang L / Junjie H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Preclinical development of GR2002, a novel anti-TSLP bispecific antibody with potent TSLP inhibitory effects
Authors: Zhigang L / Junjie H / Hongtao Q
History
DepositionMay 7, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60046.png

Downloads & links

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Map

FileDownload / File: emd_60046.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.491
Minimum - Maximum-2.5667748 - 3.868613
Average (Standard dev.)0.00075517845 (±0.07145881)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60046_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60046_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_60046_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 : GR2002-F(ab')2: TSLP complex

EntireName: GR2002-F(ab')2: TSLP complex
Components
  • Complex: GR2002-F(ab')2: TSLP complex
    • Protein or peptide: Fab-H1A10 fragment, heavy chain
    • Protein or peptide: Fab fragment, light chain
    • Protein or peptide: Thymic stromal lymphopoietin
    • Protein or peptide: Fab-H3B10 fragment, heavy chain

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Supramolecule #1: GR2002-F(ab')2: TSLP complex

SupramoleculeName: GR2002-F(ab')2: TSLP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fab-H1A10 fragment, heavy chain

MacromoleculeName: Fab-H1A10 fragment, heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.520986 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYAFS NYWMNWVRQA PGQGLEWMGQ IFPGDSDTDY DQKFQGRVTM TRDTSTSTVY MELSSLRSE DTAVYYCARA GYYRGYYAMD YWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYAFS NYWMNWVRQA PGQGLEWMGQ IFPGDSDTDY DQKFQGRVTM TRDTSTSTVY MELSSLRSE DTAVYYCARA GYYRGYYAMD YWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSCDKTH TCPPCPAPEF EG GPSVFLF PPKPKDTLMI SRTPEVT

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Macromolecule #2: Fab fragment, light chain

MacromoleculeName: Fab fragment, light chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.398883 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EIVMTQSPAT LSVSPGERAT LSCSVSSSIS SSNLHWYQQK PGQAPRPWIY GTSNLASGIP ARFSGSGSGT EFTLTISSVQ AEDFAVYYC QQWSSYPLTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVMTQSPAT LSVSPGERAT LSCSVSSSIS SSNLHWYQQK PGQAPRPWIY GTSNLASGIP ARFSGSGSGT EFTLTISSVQ AEDFAVYYC QQWSSYPLTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #3: Thymic stromal lymphopoietin

MacromoleculeName: Thymic stromal lymphopoietin / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.452688 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
YDFTNCDFEK IKAAYLSTIS KDLITYMSGT KSTEFNNTVS CSNRPHCLTE IQSLTFNPTA GCASLAKEMF AMKTKAALAI WCPGYSETQ INATQAMKKR RKRKVTTNKC LEQVSQLQGL WRRFNRPL

UniProtKB: Thymic stromal lymphopoietin

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Macromolecule #4: Fab-H3B10 fragment, heavy chain

MacromoleculeName: Fab-H3B10 fragment, heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.585062 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVTLKESGPV LVKPTETLTL TCTVSGFSLS SYDISWIRQP PGKALEWLGV IWSEGGTSYS TSLKSRLTIS KDTSKSQVVL TMTNMDPVD TATYYCARDS DDGYLNWGQG TLVTVSSAST KGPSVFPLAP SSKSTSEGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String:
QVTLKESGPV LVKPTETLTL TCTVSGFSLS SYDISWIRQP PGKALEWLGV IWSEGGTSYS TSLKSRLTIS KDTSKSQVVL TMTNMDPVD TATYYCARDS DDGYLNWGQG TLVTVSSAST KGPSVFPLAP SSKSTSEGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVDHKPSNT KVDKTVEPKS CDKTHTCPPC PAPEFEGGPS VF LFPPKPK DTLMISRTPE VT

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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: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147296
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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