9YKM | pdb_00009ykm

Crystal structure of apo-human Mincle

• PDB DOI: https://doi.org/10.2210/pdb9YKM/pdb

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


• Deposited: 2025-10-07 Released: 2026-10-21 
• Deposition Author(s): Riel, A.M.S., Yates-Hansen, C.K., McClelland, L.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.188 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of apo-human Mincle

Riel, A.M.S., Yates-Hansen, C.K., McClelland, L.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.96 kDa 
• Atom Count: 1,225 
• Modeled Residue Count: 132 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 4 member E	A	147	Homo sapiens	Mutation(s): 0  Gene Names: CLEC4E, CLECSF9, MINCLE, UNQ218/PRO244
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULY5 (Homo sapiens) Explore Q9ULY5  Go to UniProtKB:  Q9ULY5
PHAROS:  Q9ULY5 GTEx:  ENSG00000166523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.188 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.166	α = 90
b = 49.166	β = 90
c = 43.67	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-21 
Deposition Author(s): Riel, A.M.S., Yates-Hansen, C.K., McClelland, L.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM140963
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93023C00047

Revision History  

• Version 1.0: 2026-10-21
  Type: Initial release