5WJF | pdb_00005wjf

Crystal structure of murine 4-1BB from HEK293T cells in P21212 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.288 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of murine 4-1BB and its interaction with 4-1BBL support a role for galectin-9 in 4-1BB signaling.

Bitra, A.Doukov, T.Wang, J.Picarda, G.Benedict, C.A.Croft, M.Zajonc, D.M.

(2018) J Biological Chem 293: 1317-1329

  • DOI: https://doi.org/10.1074/jbc.M117.814905
  • Primary Citation Related Structures: 
    5WI8, 5WIW, 5WJF

  • PubMed Abstract: 

    4-1BB (CD137) is a TNF receptor superfamily (TNFRSF) member that is thought to undergo receptor trimerization upon binding to its trimeric TNF superfamily ligand (4-1BBL) to stimulate immune responses. 4-1BB also can bind to the tandem repeat-type lectin galectin-9 (Gal-9), and signaling through mouse (m)4-1BB is reduced in galectin-9 (Gal-9)-deficient mice, suggesting a pivotal role of Gal-9 in m4-1BB activation. Here, using sulfur-SAD phasing, we determined the crystal structure of m4-1BB to 2.2-Å resolution. We found that similar to other TNFRSFs, m4-1BB has four cysteine-rich domains (CRDs). However, the organization of CRD1 and the orientation of CRD3 and CRD4 with respect to CRD2 in the m4-1BB structure distinctly differed from those of other TNFRSFs. Moreover, we mapped two Asn residues within CRD4 that are N -linked glycosylated and mediate m4-1BB binding to Gal-9. Kinetics studies of m4-1BB disclosed a very tight nanomolar binding affinity to m4-1BBL with an unexpectedly strong avidity effect. Both N- and C-terminal domains of Gal-9 bound m4-1BB, but with lower affinity compared with m4-1BBL. Although the TNF homology domain (THD) of human (h)4-1BBL forms non-covalent trimers, we found that m4-1BBL formed a covalent dimer via 2 cysteines absent in h4-1BBL. As multimerization and clustering is a prerequisite for TNFR intracellular signaling, and as m4-1BBL can only recruit two m4-1BB monomers, we hypothesize that m4-1BBL and Gal-9 act together to aid aggregation of m4-1BB monomers to efficiently initiate m4-1BB signaling.


  • Organizational Affiliation
    • From the Division of Immune Regulation, La Jolla Institute for Allergy and Immunology (LJI), La Jolla, California 92037.

Macromolecule Content 

  • Total Structure Weight: 31.92 kDa 
  • Atom Count: 2,117 
  • Modeled Residue Count: 269 
  • Deposited Residue Count: 286 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 9
A, B
143Mus musculusMutation(s): 0 
Gene Names: Tnfrsf9Cd137IlaLy63
UniProt & NIH Common Fund Data Resources
Find proteins for P20334 (Mus musculus)
Explore P20334 
Go to UniProtKB:  P20334
IMPC:  MGI:1101059
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20334
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P20334-1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.288 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.05α = 90
b = 67.76β = 90
c = 87.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUCCANEERmodel building
ARP/wARPmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary