6P67 | pdb_00006p67

Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha 2B8 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.266 (Depositor) 
  • R-Value Work: 
    0.249 (Depositor) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

New anti-IL-7R alpha monoclonal antibodies show efficacy against T cell acute lymphoblastic leukemia in pre-clinical models.

Hixon, J.A.Andrews, C.Kashi, L.Kohnhorst, C.L.Senkevitch, E.Czarra, K.Barata, J.T.Li, W.Schneider, J.P.Walsh, S.T.R.Durum, S.K.

(2020) Leukemia 34: 35-49

  • DOI: https://doi.org/10.1038/s41375-019-0531-8
  • Primary Citation Related Structures: 
    6P4Y, 6P50, 6P67

  • PubMed Abstract: 

    Pediatric T cell acute lymphoblastic leukemia (T-ALL) cells frequently contain mutations in the interleukin-7 (IL-7) receptor pathway or respond to IL-7 itself. To target the IL-7 receptor on T-ALL cells, murine monoclonal antibodies (MAbs) were developed against the human IL-7Rα chain and chimerized with human IgG1 constant regions. Crystal structures demonstrate that the two MAbs bound different IL-7Rα epitopes. The MAbs mediated antibody-dependent cell-mediated cytotoxicity (ADCC) against patient-derived xenograft (PDX) T-ALL cells, which was improved by combining two MAbs. In vivo, the MAbs showed therapeutic efficacy via ADCC-dependent and independent mechanisms in minimal residual and established disease. PDX T-ALL cells that relapsed following a course of chemotherapy displayed elevated IL-7Rα, and MAb treatment is effective against relapsing disease, suggesting the use of anti-IL7Rα MAbs in relapsed T-ALL patients or patients that do not respond to chemotherapy.


  • Organizational Affiliation
    • Cytokines and Immunity Section, Cancer and Inflammation Program (CIP), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 296.91 kDa 
  • Atom Count: 19,325 
  • Modeled Residue Count: 2,512 
  • Deposited Residue Count: 2,648 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-IL-7R 2B8 Fab heavy chain
A, C, E, H
225Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-IL-7R 2B8 Fab light chain
B, D, F, L
214Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-7 receptor subunit alpha
G, I, J, K
223Homo sapiensMutation(s): 0 
Gene Names: IL7R
UniProt & NIH Common Fund Data Resources
Find proteins for P16871 (Homo sapiens)
Explore P16871 
Go to UniProtKB:  P16871
PHAROS:  P16871
GTEx:  ENSG00000168685 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16871
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P16871-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, N
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.266 (Depositor) 
  • R-Value Work:  0.249 (Depositor) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.9α = 90
b = 219.68β = 104.328
c = 90.35γ = 90
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2020-01-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-03-13
    Changes: Source and taxonomy
  • Version 2.3: 2024-10-23
    Changes: Structure summary