9HLL | pdb_00009hll

murine aM I-domain in complex with nanobody aCR3


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
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Three cryo-EM structures of complement C3d-bound alpha M beta 2 reveal an unexpected layer of dynamics for alpha I-containing integrin receptors.

Lorentzen, J.Fruergaard, M.U.Lukacsi, S.Jorgensen, M.H.van Veghel, T.L.G.Jensen, R.K.Pietrzak-Lichwa, K.J.Bajtay, Z.Horejsi, V.Flygaard, R.K.Vorselen, D.Mortensen, S.A.Andersen, G.R.

(2026) Sci Adv 12: eaea7241-eaea7241

  • DOI: https://doi.org/10.1126/sciadv.aea7241
  • Primary Citation Related Structures: 
    9GMU, 9HLL, 9RM9, 9RMA, 9T3Y, 9T5V, 9T5W, 9T5Z

  • PubMed Abstract: 

    Integrins are heterodimeric membrane proteins acting as mechanosensing receptors. Nine human α-subunits contain a ligand binding αI domain, but how ligands activate αI integrins are not understood. We present cryo-EM structures of the αI integrin α M β 2 in complex with the C3d ligand. The ligand-bound αI domain appears to have two major opposite orientations relative to the β 2 subunit. Ligand binding induces an ordered conformation of the α M internal ligand region that is tightly packed between the α M β-propeller and the β 2 βI-domain. Recognition of the internal ligand induces an open βI conformation practically identical to that of ligand-bound αI-less integrins confirming that ligand binding and signaling are coupled by a universal mechanism across all integrins. Integration of our findings with prior data allows us to propose a model for C3dg/iC3b-bound α M β 2 in the phagocytotic cup and outline mechanistic models for external ligand-induced activation of α M β 2 .


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Aarhus University, Aarhus, DK8000, Denmark.

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

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin alpha-M198Mus musculusMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05555
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
aCR3 nanobody
B, C, D
130Lama glamaMutation(s): 0 

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 = 78.402α = 90
b = 127.444β = 90
c = 125.855γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateLeo LF-OC-22-001076
Other privateDenmarkAlexion Discovery RN7049
Other governmentDenmarkFNU 3103-00009B

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-07-01
    Changes: Database references