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- EMDB-63505: antibody 20G5 (Fab')2 in complex with human B7-H3 -

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Basic information

Entry
Database: EMDB / ID: EMD-63505
Titleantibody 20G5 (Fab')2 in complex with human B7-H3
Map data
Sample
  • Complex: antibody 20G5 (Fab')2 in complex with human B7-H3
    • Protein or peptide: antibody 20G5 Fab heavy chain
    • Protein or peptide: antibody 20G5 Fab light chain
    • Protein or peptide: CD276 antigen
KeywordsB7-H3 / antibody / complex / ANTITUMOR PROTEIN/IMMUNE SYSTEM / ANTITUMOR PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of immune response / regulation of cytokine production / positive regulation of T cell proliferation / T cell activation / positive regulation of type II interferon production / T cell receptor signaling pathway / signaling receptor binding / external side of plasma membrane / membrane
Similarity search - Function
: / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...: / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / 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: 3.67 Å
AuthorsLi B / Zhou S / He K
Funding support China, 1 items
OrganizationGrant numberCountry
Other private China
CitationJournal: Nat Commun / Year: 2026
Title: B7-H3-mediated cis-inhibition of EGFR by a tumor-selective bispecific antibody enhances anti-tumor efficacy and minimizes toxicities.
Authors: Jian Guan / Tiongsun Chia / Bin Li / Tianyu Zhu / Zhengguang Liao / Junjie Deng / Fenggen Fu / Weiwei Wu / Chengtao Liu / Ya Liu / Ninghuan Li / Lili Yue / Lei Cao / Jia Lu / Mengjia Zhu / ...Authors: Jian Guan / Tiongsun Chia / Bin Li / Tianyu Zhu / Zhengguang Liao / Junjie Deng / Fenggen Fu / Weiwei Wu / Chengtao Liu / Ya Liu / Ninghuan Li / Lili Yue / Lei Cao / Jia Lu / Mengjia Zhu / Xiaomin Ling / Huilin Zheng / Shuming Lin / Li Li / Shuaixiang Zhou / Kaijie He /
Abstract: Therapeutic targeting of epidermal growth factor receptor (EGFR) in solid tumors faces significant limitations due to on-target/off-tumor toxicities, underscoring the urgent need for tumor-selective ...Therapeutic targeting of epidermal growth factor receptor (EGFR) in solid tumors faces significant limitations due to on-target/off-tumor toxicities, underscoring the urgent need for tumor-selective anti-EGFR therapies. Comprehensive bioinformatics and histopathological analyses identify marked upregulation of B7-H3 across EGFR-positive malignancies, contrasting with its minimal expression in healthy tissues. Leveraging an unbiased functional screen of bispecific antibodies (bsAbs) combining diverse B7-H3 and EGFR binders, we develop IBI334, a EGFR/B7-H3 bsAb exhibiting exceptional tumor selectivity. In preclinical models, IBI334 outperforms conventional EGFR antibodies by demonstrating superior EGFR occupancy, enhanced ligand-blocking efficacy, accelerated receptor degradation, and potent suppression of downstream EGFR signaling. Mechanistic studies demonstrate B7-H3-mediated cis-inhibition. The human B7-H3 extracellular domain (ECD) in complex with anti-B7-H3 Fab is resolved by cryo-EM, revealing critical residues for the antibody-B7-H3 interaction. IBI334 demonstrates robust antitumor activity in vitro and in vivo across EGFR-driven tumor models and synergized effectively with KRAS inhibitors. Toxicological evaluations in non-human primates reveals a favorable safety profile, with no EGFR-related adverse effects observed at doses up to 120 mg/kg over 4 weeks. Supported by these preclinical findings, IBI334 has advanced to a phase 1 clinical trial (NCT05774873) for advanced/metastatic solid tumors.
History
DepositionFeb 19, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63505.png

Downloads & links

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Map

FileDownload / File: emd_63505.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 440 pix.
= 326.92 Å		0.74 Å/pix.
x 440 pix.
= 326.92 Å		0.74 Å/pix.
x 440 pix.
= 326.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.4443758 - 0.7867233
Average (Standard dev.)-0.000027914699 (±0.008896704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 326.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63505_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_63505_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 : antibody 20G5 (Fab')2 in complex with human B7-H3

EntireName: antibody 20G5 (Fab')2 in complex with human B7-H3
Components
  • Complex: antibody 20G5 (Fab')2 in complex with human B7-H3
    • Protein or peptide: antibody 20G5 Fab heavy chain
    • Protein or peptide: antibody 20G5 Fab light chain
    • Protein or peptide: CD276 antigen

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Supramolecule #1: antibody 20G5 (Fab')2 in complex with human B7-H3

SupramoleculeName: antibody 20G5 (Fab')2 in complex with human B7-H3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 145 kDa/nm

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Macromolecule #1: CD276 antigen

MacromoleculeName: CD276 antigen / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.544859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LEVQVPEDPV VALVGTDATL CCSFSPEPGF SLAQLNLIWQ LTDTKQLVHS FAEGQDQGSA YANRTALFPD LLAQGNASLR LQRVRVADE GSFTCFVSIR DFGSAAVSLQ VAAPYSKPSM TLEPNKDLRP GDTVTITCSS YQGYPEAEVF WQDGQGVPLT G NVTTSQMA ...String:
LEVQVPEDPV VALVGTDATL CCSFSPEPGF SLAQLNLIWQ LTDTKQLVHS FAEGQDQGSA YANRTALFPD LLAQGNASLR LQRVRVADE GSFTCFVSIR DFGSAAVSLQ VAAPYSKPSM TLEPNKDLRP GDTVTITCSS YQGYPEAEVF WQDGQGVPLT G NVTTSQMA NEQGLFDVHS ILRVVLGANG TYSCLVRNPV LQQDAHSSVT ITPQRSPTGA VEVQVPEDPV VALVGTDATL RC SFSPEPG FSLAQLNLIW QLTDTKQLVH SFTEGRDQGS AYANRTALFP DLLAQGNASL RLQRVRVADE GSFTCFVSIR DFG SAAVSL QVAAPYSKPS MTLEPNKDLR PGDTVTITCS SYRGYPEAEV FWQDGQGVPL TGNVTTSQMA NEQGLFDVHS VLRV VLGAN GTYSCLVRNP VLQQDAHGSV TITGQPMT

UniProtKB: CD276 antigen

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Macromolecule #2: antibody 20G5 Fab heavy chain

MacromoleculeName: antibody 20G5 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.274547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYTFT EYIMHWVRQA PGQRLEWMGG INPGTGGTTY NQKFKDRVTI TVDTSASTAY MELSSLRSE DTAVYYCTRR TPPWHFAVWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT EYIMHWVRQA PGQRLEWMGG INPGTGGTTY NQKFKDRVTI TVDTSASTAY MELSSLRSE DTAVYYCTRR TPPWHFAVWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLG

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Macromolecule #3: antibody 20G5 Fab light chain

MacromoleculeName: antibody 20G5 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.293787 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLTQSPSF LSASVGDRVT ITCSASSSVS YIHWYQQKPG KAPKRWIYDT SRLASGVPSR FSGSGSGTEF TLTISSLQPE DFATYYCQQ WSSAPLTFGG GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
DIQLTQSPSF LSASVGDRVT ITCSASSSVS YIHWYQQKPG KAPKRWIYDT SRLASGVPSR FSGSGSGTEF TLTISSLQPE DFATYYCQQ WSSAPLTFGG GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 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 ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 109088
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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