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- PDB-35tl: PD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5 -

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Basic information

Entry
Database: PDB / ID: 35tl
TitlePD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5
Components
  • Germinal-designed anti-PD-L1 scFv H5, V(H) domain
  • Germinal-designed anti-PD-L1 scFv H5, V(L) domain
  • Programmed cell death 1 ligand 1
KeywordsDE NOVO PROTEIN / scfv / designed / binder
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 speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsZhang, J.L. / Rao, B. / Feng, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Nat Biotechnol / Year: 2026
Title: Efficient generation of epitope-targeted antibodies with Germinal.
Authors: Luis S Mille-Fragoso / Claudia L Driscoll / John N Wang / Haoyu Dai / Talal Widatalla / Jim L Zhang / Xiaowei Zhang / Bing Rao / Liang Feng / Brian L Hie / Xiaojing J Gao /
Abstract: Obtaining antibodies to specific protein targets is a widely important yet experimentally laborious process. Meanwhile, computational methods for antibody design have been limited by low success ...Obtaining antibodies to 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 require resource-intensive screening. Here we introduce Germinal, a broadly enabling generative pipeline 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 de novo design of functional complementarity-determining regions onto a user-specified structural framework. When tested against four diverse protein targets, Germinal designed functional antibodies across all targets and binder formats, testing only 43-101 designs for each antigen. Validated designs also exhibited robust expression in mammalian cells and high sequence and structural novelty. We provide open-source code and full computational and experimental protocols to facilitate wide adoption.
#1: Journal: 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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
B: Germinal-designed anti-PD-L1 scFv H5, V(H) domain
C: Germinal-designed anti-PD-L1 scFv H5, V(L) domain


Theoretical massNumber of molelcules
Total (without water)80,6033
Polymers80,6033
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 33318.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Homo sapiens (human) / References: UniProt: Q9NZQ7
#2: Antibody Germinal-designed anti-PD-L1 scFv H5, V(H) domain


Mass: 23806.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#3: Antibody Germinal-designed anti-PD-L1 scFv H5, V(L) domain


Mass: 23478.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PD-L1 complexed with Germinal-designed anti-PD-L1 scFv H5
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Topazparticle selection
13cryoSPARC3D reconstruction
14PHENIX1.21.2_5419model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94644 / Symmetry type: POINT
RefinementHighest resolution: 3.93 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0052727
ELECTRON MICROSCOPYf_angle_d1.053695
ELECTRON MICROSCOPYf_dihedral_angle_d5.532375
ELECTRON MICROSCOPYf_chiral_restr0.058411
ELECTRON MICROSCOPYf_plane_restr0.008468

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