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- EMDB-77181: PD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5 -

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Basic information

Entry
Database: EMDB / ID: EMD-77181
TitlePD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5
Map datasharpened map
Sample
  • Complex: PD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5
    • Protein or peptide: Programmed cell death 1 ligand 1
    • Protein or peptide: Germinal-designed anti-PD-L1 scFv H5, V(H) domain
    • Protein or peptide: Germinal-designed anti-PD-L1 scFv H5, V(L) domain
Keywordsscfv / designed / binder / DE NOVO PROTEIN
Function / homology
Function and homology information


negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / Regulation of PD-L1(CD274) translation / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / TRIF-dependent toll-like receptor signaling pathway / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / PD-L1(CD274) glycosylation and translocation to plasma membrane ...negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / Regulation of PD-L1(CD274) translation / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / TRIF-dependent toll-like receptor signaling pathway / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / PD-L1(CD274) glycosylation and translocation to plasma membrane / negative regulation of T cell activation / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / negative regulation of T cell receptor signaling pathway / negative regulation of T cell proliferation / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / T cell costimulation / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / SPOP-mediated proteasomal degradation of PD-L1(CD274) / positive regulation of T cell proliferation / response to cytokine / recycling endosome membrane / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / nuclear speck / immune response / receptor ligand activity / external side of plasma membrane / Golgi membrane / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciessynthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsZhang JL / Rao B / Feng L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: bioRxiv / Year: 2025
Title: Efficient generation of epitope-targeted antibodies with Germinal.
Authors: Luis S Mille-Fragoso / John N Wang / Claudia L Driscoll / Haoyu Dai / Talal Widatalla / Xiaowei Zhang / Brian L Hie / Xiaojing J Gao /
Abstract: Obtaining novel antibodies against specific protein targets is a widely important yet experimentally laborious process. Meanwhile, computational methods for antibody design have been limited by low ...Obtaining novel antibodies against specific protein targets is a widely important yet experimentally laborious process. Meanwhile, computational methods for antibody design have been limited by low success rates that currently require resource-intensive screening. Here, we introduce Germinal, a broadly enabling generative framework that designs antibodies against specific epitopes with nanomolar binding affinities while requiring only low-n experimental testing. Our method co-optimizes antibody structure and sequence by integrating a structure predictor with an antibody-specific protein language model to perform design of functional complementarity-determining regions (CDRs) onto a user-specified structural framework. When tested against four diverse protein targets, Germinal achieved an experimental success rate of 4-22% across all targets, testing only 43-101 designs for each antigen. Validated nanobodies also exhibited robust expression in mammalian cells and nanomolar binding affinities. We provide open-source code and full computational and experimental protocols to facilitate wide adoption. Germinal represents a milestone in efficient, epitope-targeted antibody design, with notable implications for the development of molecular tools and therapeutics.
History
DepositionMay 15, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77181.png

Downloads & links

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Map

FileReleased
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 288 pix.
= 282.24 Å		0.98 Å/pix.
x 288 pix.
= 282.24 Å		0.98 Å/pix.
x 288 pix.
= 282.24 Å

Surface

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.9453213 - 2.155071
Average (Standard dev.)0.00030748217 (±0.022523375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 282.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_77181_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map a

Fileemd_77181_half_map_1.map
Annotationhalf map a
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map b

Fileemd_77181_half_map_2.map
Annotationhalf map b
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : PD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5

EntireName: PD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5
Components
  • Complex: PD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5
    • Protein or peptide: Programmed cell death 1 ligand 1
    • Protein or peptide: Germinal-designed anti-PD-L1 scFv H5, V(H) domain
    • Protein or peptide: Germinal-designed anti-PD-L1 scFv H5, V(L) domain

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Supramolecule #1: PD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5

SupramoleculeName: PD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Programmed cell death 1 ligand 1

MacromoleculeName: Programmed cell death 1 ligand 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.318312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRIFAVFIFM TYWHLLNAFT VTVPKDLYVV EYGSNMTIEC KFPVEKQLDL AALIVYWEME DKNIIQFVHG EEDLKVQHSS YRQRARLLK DQLSLGNAAL QITDVKLQDA GVYRCMISYG GADYKRITVK VNAPYNKINQ RILVVDPVTS EHELTCQAEG Y PKAEVIWT ...String:
MRIFAVFIFM TYWHLLNAFT VTVPKDLYVV EYGSNMTIEC KFPVEKQLDL AALIVYWEME DKNIIQFVHG EEDLKVQHSS YRQRARLLK DQLSLGNAAL QITDVKLQDA GVYRCMISYG GADYKRITVK VNAPYNKINQ RILVVDPVTS EHELTCQAEG Y PKAEVIWT SSDHQVLSGK TTTTNSKREE KLFNVTSTLR INTTTNEIFY CTFRRLDPEE NHTAELVIPE LPLAHPPNER TH LVILGAI LLCLGVALTF IFRLRKGRMM DVKKCGIQDT NSKKQSDTHL EET

UniProtKB: Programmed cell death 1 ligand 1

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Macromolecule #2: Germinal-designed anti-PD-L1 scFv H5, V(H) domain

MacromoleculeName: Germinal-designed anti-PD-L1 scFv H5, V(H) domain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.806922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASSIDLE MYKIHWVRQA PGKGLEWVAR INVGFDVTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCWPY SIVMLPFHGY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
EVQLVESGGG LVQPGGSLRL SCAASSIDLE MYKIHWVRQA PGKGLEWVAR INVGFDVTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCWPY SIVMLPFHGY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSC

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Macromolecule #3: Germinal-designed anti-PD-L1 scFv H5, V(L) domain

MacromoleculeName: Germinal-designed anti-PD-L1 scFv H5, V(L) domain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.478154 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQDVG KDVAWYQQKP GKAPKLLIYY YKFLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCL NANTGGITFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQDVG KDVAWYQQKP GKAPKLLIYY YKFLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCL NANTGGITFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 7.4
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: 50.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 94644
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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