9FE1 | pdb_00009fe1

Cryo-EM structure of the ternary DARPin NY_1/HLA-A0201/NY-ESO1 complex.

• PDB DOI: https://doi.org/10.2210/pdb9FE1/pdb
• EM Map EMD-50336: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-17 Released: 2025-05-28 
• Deposition Author(s): Schulte, T., Wallden, K., Carroni, M., Sandalova, T., Walser, M., Mueller, S., Venetz, N., Achour, A.
• Funding Organization(s): Knut and Alice Wallenberg Foundation, Cancerfonden, Swedish Research Council

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Development of highly specific and potent HLA/peptide-targeting DARPin T cell engagers

Venetz, N., Schulte, T., Mueller, S., Wallden, K., Fischer, S., Kadri, N., Paladino, M., Pina, N., Radom, F., Villemagne, D., Bruckmaier, S., Cornelius, A., Hospodarsch, T., Sun, R., Chambers, B.J., Carroni, M., Levitsky, V., Sandalova, T., Walser, M., Achour, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy, gel filtration

Macromolecule Content 

• Total Structure Weight: 65.11 kDa 
• Atom Count: 4,295 
• Modeled Residue Count: 539 
• Deposited Residue Count: 575 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	291	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for Q8WLS4 (Homo sapiens) Explore Q8WLS4  Go to UniProtKB:  Q8WLS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cancer/testis antigen 1	C	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P78358 (Homo sapiens) Explore P78358  Go to UniProtKB:  P78358
PHAROS:  P78358 GTEx:  ENSG00000184033 ENSG00000268651

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin NY_1	D	175	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Schulte, T., Wallden, K., Carroni, M., Sandalova, T., Walser, M., Mueller, S., Venetz, N., Achour, A.

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Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	--
Cancerfonden	Sweden	--
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release