8VOI | pdb_00008voi

HADDOCK models of active human alphaM I-domain bound to the the C-terminal domain of the cytokine pleiotrophin

  • Classification: CELL ADHESION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-01-15 Released: 2024-05-15 
  • Deposition Author(s): Wang, X., Nguyen, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

alpha M I-domain of integrin Mac-1 binds the cytokine pleiotrophin using multiple mechanisms.

Nguyen, H.Podolnikova, N.P.Ugarova, T.P.Wang, X.

(2024) Structure 32: 1184-1196.e4

  • DOI: https://doi.org/10.1016/j.str.2024.04.013
  • Primary Citation of Related Structures:  
    8VOH, 8VOI

  • PubMed Abstract: 

    The integrin Mac-1 (α M β 2 , CD11b/CD18, CR3) is an adhesion receptor expressed on macrophages and neutrophils. Mac-1 is also a promiscuous integrin that binds a diverse set of ligands through its α M I-domain. However, the binding mechanism of most ligands remains unclear. We have characterized the interaction of α M I-domain with the cytokine pleiotrophin (PTN), a protein known to bind α M I-domain and induce Mac-1-mediated cell adhesion and migration. Our data show that PTN's N-terminal domain binds a unique site near the N- and C-termini of the α M I-domain using a metal-independent mechanism. However, a stronger interaction is achieved when an acidic amino acid in a zwitterionic motif in PTN's C-terminal domain chelates the divalent cation in the metal ion-dependent adhesion site of active α M I-domain. These results indicate that α M I-domain can bind ligands using multiple mechanisms and that the active α M I-domain has a preference for motifs containing both positively and negatively charged amino acids.


  • Organizational Affiliation
    • School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-M184Homo sapiensMutation(s): 0 
Gene Names: ITGAMCD11BCR3A
UniProt & NIH Common Fund Data Resources
Find proteins for P11215 (Homo sapiens)
Explore P11215 
Go to UniProtKB:  P11215
PHAROS:  P11215
GTEx:  ENSG00000169896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11215
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotrophin57Homo sapiensMutation(s): 0 
Gene Names: PTNHBNF1NEGF1
UniProt & NIH Common Fund Data Resources
Find proteins for P21246 (Homo sapiens)
Explore P21246 
Go to UniProtKB:  P21246
PHAROS:  P21246
GTEx:  ENSG00000105894 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21246
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • 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 of General Medical Sciences (NIH/NIGMS)United StatesGM118518
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL063199

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Structure summary
  • Version 1.2: 2025-05-28
    Changes: Database references