9HLL | pdb_00009hll

murine aM I-domain in complex with nanobody aCR3

• PDB DOI: https://doi.org/10.2210/pdb9HLL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-05 Released: 2025-12-17 
• Deposition Author(s): Fruergaard, M.U., Andersen, G.R.
• Funding Organization(s): Other private, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

murine aM I-domain in complex with nanobody aCR3

Fruergaard, M.U., Andersen, G.R.

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: isothermal titration calorimetry, gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 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 - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.98 kDa 
• Atom Count: 4,407 
• Modeled Residue Count: 550 
• Deposited Residue Count: 588 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-M	A	198	Mus musculus	Mutation(s): 0  Gene Names: Itgam
UniProt & NIH Common Fund Data Resources
Find proteins for P05555 (Mus musculus) Explore P05555  Go to UniProtKB:  P05555
IMPC:  MGI:96607

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
aCR3 nanobody	B, C, D	130	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	E [auth D], F [auth D], G [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.402	α = 90
b = 127.444	β = 90
c = 125.855	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Fruergaard, M.U., Andersen, G.R.

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Funding Organization	Location	Grant Number
Other private		Leo LF-OC-22-001076
Other private	Denmark	Alexion Discovery RN7049
Other government	Denmark	FNU 3103-00009B

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release