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- PDB-9t9m: Tilvestamab Fab bound to the anti-Fab nanobody -

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Basic information

Entry
Database: PDB / ID: 9t9m
TitleTilvestamab Fab bound to the anti-Fab nanobody
Components
  • Anti Nab-Fab nanobody
  • Heavy chain of BGB149 antibody
  • Light chain of BGB149 antibody
KeywordsANTITUMOR PROTEIN / anti-AXL / monoclonal antibody / cancer / AXL is a receptor tyrosine kinase
Biological speciesMus sp. (mice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsLopez, A.J. / Christakou, E. / Kursula, P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council311399 Norway
CitationJournal: ACS Omega / Year: 2026
Title: Structural Analysis of Tilvestamab in Complex with AXL.
Authors: Eleni Christakou / Andrea J Lopez / Gopinath Muruganandam / David Micklem / James B Lorens / Petri Kursula /
Abstract: AXL is a receptor tyrosine kinase with a significant role in various biological processes and important medical implications, particularly in cancer. AXL transduces signals from the extracellular ...AXL is a receptor tyrosine kinase with a significant role in various biological processes and important medical implications, particularly in cancer. AXL transduces signals from the extracellular environment into the cytoplasm by binding to its ligand, growth arrest-specific protein 6 (GAS6). Activation of AXL leads to autophosphorylation of its intracellular domain and subsequent activation of downstream signaling pathways involved in cell proliferation, migration, differentiation, and survival. Tilvestamab (also known as BGB149) is a first-in-class, humanized, therapeutic anti-AXL function-blocking monoclonal antibody. We carried out a structural characterization of the AXL-tilvestamab complex using both negative-stain and cryogenic transmission electron microscopy as well as synchrotron small-angle X-ray scattering. While AXL-Fc was highly elongated and formed large heterogeneous complexes with the full antibody, homogeneous samples for structural studies could be made using the monomeric soluble AXL extracellular domain, the Fab fragment of tilvestamab, and an anti-Fab nanobody. Both SAXS and cryo-EM confirmed successful complex formation between the three proteins, and a low-resolution 3D model for the tilvestamab-AXL complex is presented. The data allow for sample optimization for high-resolution structural biology, as well as designing mutations that could alter binding affinity and specificity.
History
DepositionNov 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 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

Downloads & links

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Assembly

Deposited unit
L: Light chain of BGB149 antibody
K: Anti Nab-Fab nanobody
H: Heavy chain of BGB149 antibody


Theoretical massNumber of molelcules
Total (without water)60,7953
Polymers60,7953
Non-polymers00
Water00
1


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

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Components

#1: Antibody Light chain of BGB149 antibody


Mass: 23872.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Light chain cleaved from the full-length BGB149 antibody using papain
Source: (natural) Mus sp. (mice)
#2: Antibody Anti Nab-Fab nanobody


Mass: 13390.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Anti Nab-Fab nanobody / Source: (natural) Mus sp. (mice)
#3: Antibody Heavy chain of BGB149 antibody


Mass: 23531.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Heavy chain cleaved from the full-length BGB149 antibody using papain
Source: (natural) Mus sp. (mice)
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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Tilvestamab Fab and the antiNabFab nanobodyCOMPLEXFab fragment of tilvestamab (BGB149, BerGenBio, Norway), a humanized AXL monoclonal antibody (light and heavy chain), it was coupled with an anti-Nab-Fab nanobody recombinant expressed in E. coliall0RECOMBINANT
2Fab fragment of tilvestamabCOMPLEXFab fragment of tilvestamab (BGB149, BerGenBio, Norway), a humanized AXL monoclonal antibody (light and heavy chain)#1-#21NATURAL
3anti nab-fab nanobody, synthetic geneCOMPLEXsynthetic gene recombinant expressed in E. coli#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.0608 MDaNO
210.048 MDaYES
310.0134 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
21Escherichia coli (E. coli)562BL21pTH27
32Escherichia coli (E. coli)562BL21pTH27
43Escherichia coli (E. coli)562BL21pTH27
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMsodium chlorideNaCl1
30.5 mMTCEPTris(2-carboxyethyl)phosphine1
SpecimenConc.: 0.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: DIFFRACTION / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 59.597 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 17189
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7UCSF ChimeraX1.1model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1244782
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1316916 / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Accession code: 7pij / Initial refinement model-ID: 1 / PDB-ID: 7pij

7pij

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-ID
1KK
2LL
3HH
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00374266
ELECTRON MICROSCOPYf_angle_d0.59085796
ELECTRON MICROSCOPYf_chiral_restr0.0437636
ELECTRON MICROSCOPYf_plane_restr0.0071750
ELECTRON MICROSCOPYf_dihedral_angle_d5.6632598

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