9ECM | pdb_00009ecm

Structure of the human integrin alphaX transmembrane domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 26 
  • Conformers Submitted: 21 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report

Validation slider image for 9ECM

This is version 1.1 of the entry. See complete history

Literature

Functional unfolding of the integrin alpha X transmembrane helix.

Vu, H.N.Lee, M.Situ, A.J.An, W.Ley, K.Kim, C.Ulmer, T.S.

(2025) Proc Natl Acad Sci U S A 122: e2507966122-e2507966122

  • DOI: https://doi.org/10.1073/pnas.2507966122
  • Primary Citation Related Structures: 
    9ECL, 9ECM

  • PubMed Abstract: 

    In biological membranes, proteins face a fundamentally different environment than in water. To avoid untenable lipid contacts with polar backbone atoms, they use the continuous hydrogen bonding achieved by α-helices or β-barrels to traverse membranes. Here, we show that integrin αX, and by homology αM, undermine this paradigm by partially unfolding the N-terminal third of their transmembrane (TM) helix. Unfolding results in a dynamic, frayed helix that weakens the association with its partnering β2 subunit to lower the activation threshold of integrin αXβ2-mediated cell adhesion. The extent of unfolding depends on membrane geometry, thereby establishing a mechanism for sensing membrane properties. The combination of adhesive control with sensory capacity in integrin αXβ2 and αMβ2 may achieve membrane localization-dependent receptor activation in leukocyte phagocytosis. The unfolding of the αX TM helix arises from a high number of α-helix-destabilizing residues that TM helices in general approach but do not exceed. Accordingly, backbone dynamics of TM helices may disrupt hydrogen bonds, modulate protein function, and optimize TM helix rigidity.


  • Organizational Affiliation
    • Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033.

Macromolecule Content 

  • Total Structure Weight: 4.64 kDa 
  • Atom Count: 329 
  • Modeled Residue Count: 42 
  • Deposited Residue Count: 42 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin alpha-X42Homo sapiensMutation(s): 0 
Gene Names: ITGAXCD11C
UniProt & NIH Common Fund Data Resources
Find proteins for P20702 (Homo sapiens)
Explore P20702 
Go to UniProtKB:  P20702
PHAROS:  P20702
GTEx:  ENSG00000140678 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20702
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 26 
  • Conformers Submitted: 21 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG072442

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references