9HQ5 | pdb_00009hq5

Crystal structure of Tetraspanin CD63mutant Large Extracellular Loop (LEL) in complex with sybody SB3

• PDB DOI: https://doi.org/10.2210/pdb9HQ5/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Drosophila melanogaster, Bacteria
• Mutation(s): Yes 


• Deposited: 2024-12-16 Released: 2025-11-19 
• Deposition Author(s): Nagarathinam, K., Krey, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Models: in silico, experimental

Literature

Evolutionary relationship of Tetraspanins

Nagarathinam, K., Karakulova, D., Thiyagaraj, D., Krey, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.42 kDa 
• Atom Count: 1,606 
• Modeled Residue Count: 214 
• Deposited Residue Count: 252 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD63 antigen	A	108	Homo sapiens	Mutation(s): 3  Gene Names: CD63, MLA1, TSPAN30
UniProt & NIH Common Fund Data Resources
Find proteins for P08962 (Homo sapiens) Explore P08962  Go to UniProtKB:  P08962
PHAROS:  P08962 GTEx:  ENSG00000135404

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sybody SB3	B	144	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.23	α = 90
b = 65.23	β = 90
c = 138.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Nagarathinam, K., Krey, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release