9LN2 | pdb_00009ln2

Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Complex with DMASPP

• PDB DOI: https://doi.org/10.2210/pdb9LN2/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Vicugna pacos
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-20 Released: 2025-05-14 
• Deposition Author(s): Yang, Y.Y., Yi, S.M., Zhang, M.T., Chen, C.-C., Guo, R.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.202 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Complex with DMASPP

Yang, Y.Y., Yi, S.M., Zhang, M.T., Chen, C.-C., Guo, R.-T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.44 kDa 
• Atom Count: 3,585 
• Modeled Residue Count: 382 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Butyrophylin 3	A, B	242	Vicugna pacos	Mutation(s): 0  Gene Names: Btn3
UniProt
Find proteins for A0A345DF50 (Vicugna pacos) Explore A0A345DF50  Go to UniProtKB:  A0A345DF50

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DST (Subject of Investigation/LOI)	G [auth B]	DIMETHYLALLYL S-THIOLODIPHOSPHATE C5 H12 O6 P2 S ZWFWSISPSBLNGO-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.202 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.858	α = 90
b = 67.988	β = 90
c = 134.307	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SAINT	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Yang, Y.Y., Yi, S.M., Zhang, M.T., Chen, C.-C., Guo, R.-T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82271887

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release