[English] 日本語
Yorodumi
- EMDB-60046: CryoEM structure of GR2002-F(ab')2: TSLP complex -

+
Open data


ID or keywords:

Loading...

-
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 / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / 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

-
Structure visualization

Supplemental images

emd_60046.png

Downloads & links

-
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 °

-
Supplemental data

-
Mask #1

Fileemd_60046_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60046_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60046_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
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)

+
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