9ECL | pdb_00009ecl

Structure of the human integrin beta2 transmembrane domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 21 
  • Conformers Submitted: 21 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report

Validation slider image for 9ECL

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: 4.43 kDa 
  • Atom Count: 313 
  • Modeled Residue Count: 43 
  • Deposited Residue Count: 43 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin beta-243Homo sapiensMutation(s): 0 
Gene Names: ITGB2CD18MFI7
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P05107 (Homo sapiens)
Explore P05107 
Go to UniProtKB:  P05107
PHAROS:  P05107
GTEx:  ENSG00000160255 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05107
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 21 
  • Conformers Submitted: 21 
  • Selection Criteria: all calculated structures submitted 

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