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- EMDB-55722: Tilvestamab Fab bound to the anti-Fab nanobody -

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Basic information

Entry
Database: EMDB / ID: EMD-55722
TitleTilvestamab Fab bound to the anti-Fab nanobody
Map dataTilvestamab Fab bound to the anti-Fab nanobody map
Sample
  • Complex: Tilvestamab Fab and the antiNabFab nanobody
    • Complex: Fab fragment of tilvestamab
      • Protein or peptide: Light chain of BGB149 antibody
      • Protein or peptide: Anti Nab-Fab nanobody
    • Complex: anti nab-fab nanobody, synthetic gene
    • Protein or peptide: Heavy chain of BGB149 antibody
Keywordsanti-AXL / monoclonal antibody / cancer / AXL is a receptor tyrosine kinase / ANTITUMOR PROTEIN
Biological speciesHomo sapiens (human) / Mus sp. (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsLopez AJ / Christakou E / Kursula P
Funding support Norway, 1 items
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, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55722.png

Downloads & links

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Map

FileDownload / File: emd_55722.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTilvestamab Fab bound to the anti-Fab nanobody map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 480 pix.
= 310.56 Å		0.65 Å/pix.
x 480 pix.
= 310.56 Å		0.65 Å/pix.
x 480 pix.
= 310.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.137
Minimum - Maximum-0.0017852954 - 1.9887761
Average (Standard dev.)0.00029753326 (±0.012644971)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 310.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55722_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_55722_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_55722_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tilvestamab Fab and the antiNabFab nanobody

EntireName: Tilvestamab Fab and the antiNabFab nanobody
Components
  • Complex: Tilvestamab Fab and the antiNabFab nanobody
    • Complex: Fab fragment of tilvestamab
      • Protein or peptide: Light chain of BGB149 antibody
      • Protein or peptide: Anti Nab-Fab nanobody
    • Complex: anti nab-fab nanobody, synthetic gene
    • Protein or peptide: Heavy chain of BGB149 antibody

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Supramolecule #1: Tilvestamab Fab and the antiNabFab nanobody

SupramoleculeName: Tilvestamab Fab and the antiNabFab nanobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Fab 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. coli
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.4 KDa

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Supramolecule #2: Fab fragment of tilvestamab

SupramoleculeName: Fab fragment of tilvestamab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: Fab fragment of tilvestamab (BGB149, BerGenBio, Norway), a humanized AXL monoclonal antibody (light and heavy chain)
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: anti nab-fab nanobody, synthetic gene

SupramoleculeName: anti nab-fab nanobody, synthetic gene / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: synthetic gene recombinant expressed in E. coli
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Light chain of BGB149 antibody

MacromoleculeName: Light chain of BGB149 antibody / type: protein_or_peptide / ID: 1
Details: Light chain cleaved from the full-length BGB149 antibody using papain
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 23.872523 KDa
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRSSQSLV HSNGIPYLHW YQQKPGKAPK LLIYRVSNRF SGVPSRFSGS GSGTDFTLTI SSLQPEDFA TYYCSQGTHV PPTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIQMTQSPSS LSASVGDRVT ITCRSSQSLV HSNGIPYLHW YQQKPGKAPK LLIYRVSNRF SGVPSRFSGS GSGTDFTLTI SSLQPEDFA TYYCSQGTHV PPTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE

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Macromolecule #2: Anti Nab-Fab nanobody

MacromoleculeName: Anti Nab-Fab nanobody / type: protein_or_peptide / ID: 2 / Details: Anti Nab-Fab nanobody / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 13.390644 KDa
SequenceString:
GSQVQLQESG GGLVQPGGSL RLSCAASGRT ISRYAMSWFR QAPGKEREFV AVARRSGDGA FYADSVQGRF TVSRDDAKNT VYLQMNSLK PEDTAVYYCA IDSDTFYSGS YDYWGQGTQV TVSS

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Macromolecule #3: Heavy chain of BGB149 antibody

MacromoleculeName: Heavy chain of BGB149 antibody / type: protein_or_peptide / ID: 3
Details: Heavy chain cleaved from the full-length BGB149 antibody using papain
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 23.531342 KDa
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGYSFT DFYINWVRQA PGKGLEWVAR IFPGGDNTYY NEKFKGRFTL SADTSKSTAY LQMNSLRAE DTAVYYCARR GLYYAMDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
EVQLVESGGG LVQPGGSLRL SCAASGYSFT DFYINWVRQA PGKGLEWVAR IFPGGDNTYY NEKFKGRFTL SADTSKSTAY LQMNSLRAE DTAVYYCARR GLYYAMDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KS

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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

Concentration0.33 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
0.5 mMTris(2-carboxyethyl)phosphineTCEP
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GOLD / Support film - #1 - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 17189 / Average exposure time: 1.4 sec. / Average electron dose: 59.597 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1244782
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7pij

Final reconstructionNumber classes used: 3 / Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1316916
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7pij

chain_id: K, source_name: PDB, initial_model_type: experimental model

7pij

chain_id: L, source_name: PDB, initial_model_type: experimental model

7pij

chain_id: H, source_name: PDB, initial_model_type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.10)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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