6P50 | pdb_00006p50

Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha Fab 4A10

• PDB DOI: https://doi.org/10.2210/pdb6P50/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2019-05-29 Released: 2019-09-04 
• Deposition Author(s): Walsh, S.T.R., Kashi, L., Kohnhorst, C.L.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.330 (Depositor), 0.342 (DCC) 
• R-Value Work: 
  0.285 (Depositor), 0.291 (DCC) 
• R-Value Observed: 
  0.288 (Depositor) 

Starting Models: experimental

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

• PubMed: 31439943 
• 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.

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Organizational Affiliation: 
• Cytokines and Immunity Section, Cancer and Inflammation Program (CIP), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, USA.
Comparative Biomedical Scientist Training Program, NIH, Bethesda, MD, USA.
Michigan State University, East Lansing, MI, USA.
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
Cancer Biology Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal.
Chemical Biology Laboratory, NCI, NIH, Frederick, MD, USA.
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA. [e-mail].
Chemical Biology Laboratory, NCI, NIH, Frederick, MD, USA. [e-mail].
Cytokines and Immunity Section, Cancer and Inflammation Program (CIP), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 73.88 kDa 
• Atom Count: 3,990 
• Modeled Residue Count: 522 
• Deposited Residue Count: 661 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-7 receptor subunit alpha	A [auth C]	223	Homo sapiens	Mutation(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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P16871-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-IL-7R 4A10 Fab heavy chain	B [auth H]	225	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-IL-7R 4A10 Fab light chain	C [auth L]	213	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.330 (Depositor), 0.342 (DCC) 
• R-Value Work:  0.285 (Depositor), 0.291 (DCC) 
• R-Value Observed: 0.288 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.113	α = 90
b = 40.171	β = 105.477
c = 105.097	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASES	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Walsh, S.T.R., Kashi, L., Kohnhorst, C.L.

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

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Database references
• Version 1.3: 2020-02-05
  Changes: Data collection
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.6: 2024-10-16
  Changes: Structure summary