9II6 | pdb_00009ii6

Cryo-EM structure of the intracellular domains of BTN2A1-BTN3A1-BTN3A3

• PDB DOI: https://doi.org/10.2210/pdb9II6/pdb
• EM Map EMD-60591: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-06-19 Released: 2025-06-25 
• Deposition Author(s): Gao, W., Zheng, J., Zhu, Y., Huang, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the intracellular domains of BTN2A1-BTN3A1-BTN3A3

Gao, W., Zheng, J., Zhu, Y., Huang, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 122.74 kDa 
• Atom Count: 7,975 
• Modeled Residue Count: 972 
• Deposited Residue Count: 1,057 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Butyrophilin subfamily 2 member A1	A, D [auth E]	254	Homo sapiens	Mutation(s): 0  Gene Names: BTN2A1, BT2.1, BTF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KYR7 (Homo sapiens) Explore Q7KYR7  Go to UniProtKB:  Q7KYR7
PHAROS:  Q7KYR7 GTEx:  ENSG00000112763

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Butyrophilin subfamily 3 member A1	B	239	Homo sapiens	Mutation(s): 1  Gene Names: BTN3A1, BTF5
UniProt & NIH Common Fund Data Resources
Find proteins for O00481 (Homo sapiens) Explore O00481  Go to UniProtKB:  O00481
PHAROS:  O00481 GTEx:  ENSG00000026950

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Butyrophilin subfamily 3 member A3	C [auth D]	310	Homo sapiens	Mutation(s): 0  Gene Names: BTN3A3, BTF3
UniProt & NIH Common Fund Data Resources
Find proteins for O00478 (Homo sapiens) Explore O00478  Go to UniProtKB:  O00478
PHAROS:  O00478 GTEx:  ENSG00000111801

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H6P (Subject of Investigation/LOI)	E [auth B]	(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate C5 H12 O8 P2 MDSIZRKJVDMQOQ-GORDUTHDSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20_4459:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Gao, W., Zheng, J., Zhu, Y., Huang, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release