9PI9 | pdb_00009pi9

Sacituzumab Fab bound to Trop2 Dimer

PDB DOI: https://doi.org/10.2210/pdb9PI9/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens, Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-07-10 Released: 2025-12-10
Deposition Author(s): Ferrao, R., Lansdon, E.B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The therapeutic antibody sacituzumab induces trophoblast cell-surface antigen-2 conformational rearrangement.

Ferrao, R., Zhang, J., Chou, C.C., Nieto, A., Langeslay, D., Chatterjee, M., Jin, D., Hung, M., Scott, I., Nagel, M., Xing, W., Letarte, S., Wang, J., Ambrogelly, A., Lansdon, E.B.

(2026) Structure 34: 264

PubMed: 41314216 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2025.11.002
Primary Citation Related Structures:
9PI9

PubMed Abstract:
Sacituzumab govitecan (SG) is a therapeutic antibody-drug conjugate globally approved for the treatment of breast cancer. SG targets the trophoblast cell-surface antigen-2 (Trop2) at the surface of cancer cells to deliver the cytotoxic topoisomerase I inhibitor SN-38 to the tumor microenvironment. SN-38 is covalently linked to the humanized monoclonal antibody (mAb) sacituzumab via a hydrolyzable linker. Here, we describe the 1.56-Å X-ray crystal structure and stoichiometry of the human Trop2 ectodomain in complex with a sacituzumab (hRS7) antigen-binding Fab fragment. The complex reveals a 2:2 stoichiometry where two sacituzumab Fabs bind across the two Trop2 dimer subunits, inducing a conformational change compared to the apo-structure. Cryo-electron microscopy (cryoEM) and size-exclusion chromatography in combination with multi-angle light scattering (SEC-MALS) analysis of the intact sacituzumab mAb bound to the Trop2 ECD reveals a complex whereby sacituzumab engages two Trop2 dimers in a 2:4 stoichiometry.

Organizational Affiliation

Gilead Sciences Inc., Structural Biology and Chemistry, 333 Lakeside Dr., Foster City, CA 94404, USA.

Macromolecule Content

Total Structure Weight: 153.73 kDa
Atom Count: 11,459
Modeled Residue Count: 1,315
Deposited Residue Count: 1,380
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sacituzumab Heavy Chain	A, C	226	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sacituzumab Light Chain	B, D	214	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor-associated calcium signal transducer 2	E, F	250	Homo sapiens	Mutation(s): 0 Gene Names: TACSTD2, GA733-1, M1S1, TROP2
UniProt & NIH Common Fund Data Resources
Find proteins for P09758 (Homo sapiens) Explore P09758 Go to UniProtKB: P09758
PHAROS: P09758 GTEx: ENSG00000184292
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09758
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E Focus chain F	Go to GlyGen: P09758-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain T [auth E] MOL2 format, chain T [auth E] mmCIF format, chain T [auth E]	T [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain T [auth E] Interactions & Density Focus chain T [auth E]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E]	U [auth E], W [auth F]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain U [auth E] Focus chain W [auth F]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain S [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain V [auth E] MOL2 format, chain S [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain V [auth E] mmCIF format, chain S [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth B] L [auth B] H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], Q [auth D], R [auth D], S [auth E], V [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain V [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain V [auth E]