PDB 5m5e structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

2.3Å resolution

Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor

Released: 03 May 2017

DOI: 10.2210/pdb5m5e/pdb

Source organism: Homo sapiens

Primary publication:
Cergutuzumab amunaleukin (CEA-IL2v), a CEA-targeted IL-2 variant-based immunocytokine for combination cancer immunotherapy: Overcoming limitations of aldesleukin and conventional IL-2-based immunocytokines.

Klein C, Waldhauer I, Nicolini VG, Freimoser-Grundschober A, Nayak T, Vugts DJ, Dunn C, Bolijn M, Benz J, Stihle M, Lang S, Roemmele M, Hofer T, van Puijenbroek E, Wittig D, Moser S, Ast O, Brünker P, Gorr IH, Neumann S, de Vera Mudry MC, Hinton H, Crameri F, Saro J, Evers S, Gerdes C, Bacac M, van Dongen G, Moessner E, Umaña P

Oncoimmunology 6 e1277306 (2017)

PMID: 28405498

Function and Biology Details

Biochemical function:

cytokine receptor activity

Biological process:

immune response

Cellular component:

membrane

Sequence domains:

Structure analysis Details

Assembly composition:

hetero trimer (preferred)

PDBe Complex ID:

PDB-CPX-147094 (preferred)

Entry contents:

3 distinct polypeptide molecules

Macromolecules (6 distinct):

Interleukin-2 receptor subunit beta Chain: B

Molecule details ›

Chain: B
Length: 233 amino acids
Theoretical weight: 26.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:

Canonical: P14784 (Residues: 27-240; Coverage: 41%)

Gene names: IL15RB, IL2RB
Sequence domains: Interleukin-2 receptor subunit beta N-terminal domain 1
Structure domains: Immunoglobulins

Cytokine receptor common subunit gamma Chain: C

Molecule details ›

Chain: C
Length: 259 amino acids
Theoretical weight: 30.22 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:

Canonical: P31785 (Residues: 23-262; Coverage: 69%)

Gene name: IL2RG
Sequence domains:

Structure domains: Immunoglobulins

Interleukin-2 Chain: D

Molecule details ›

Chain: D
Length: 160 amino acids
Theoretical weight: 18.18 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:

Canonical: P60568 (Residues: 8-14, 15-153; Coverage: 100%)

Gene name: IL2
Sequence domains: Interleukin 2
Structure domains: Growth Hormone; Chain: A;

Ligands and Environments

Carbohydrate polymer : NEW

Carbohydrate polymer

Carbohydrate polymer : NEW

Carbohydrate polymer

Carbohydrate polymer : NEW

Carbohydrate polymer

4 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores

X-ray source: SLS BEAMLINE X10SA

Spacegroup: P6₁

Unit cell:

a: 127.965Å b: 127.965Å c: 135.073Å

α: 90° β: 90° γ: 120°

R-values:

R R_work R_free

0.201 0.199 0.235

Expression system: Homo sapiens

Quick links

View

Close

Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
Assembly composition XML
FASTA (Entry)
Summary report (PDF)
Full report (PDF)
Percentile plot (PNG)
Percentile plot (SVG)

5m5e @ RCSB
5m5e @ PDBj
5m5e @ PDBSum
5m5e @ Proteopedia

Downloads

Close

Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
PDB file (gz)
PDBML
PDBML (ATOM lines)
PDBML (no atoms)
Structure Factors
EDS map
EDS difference map
Assembly composition XML
Assembly 1 (mmCIF; gz)
Assembly 1 (atom only; mmCIF)
FASTA (Entry)
SIFTS XML file with residue-level mappings
Summary report (PDF)
Full report (PDF)
Percentile plot (PNG)
Percentile plot (SVG)
Validation data (XML)

3D Visualisation

Citations

47 review citations

A Paradigm Shift in Cancer Immunotherapy: From Enhancement to Normalization.

Sanmamed et al. (2018)

46 more

6 mentions without citation

Cergutuzumab amunaleukin (CEA-IL2v), a CEA-targeted IL-2 variant-based immunocytokine for combination cancer immunotherapy: Overcoming limitations of aldesleukin and conventional IL-2-based immunocytokines.

Klein et al. (2017)

5 more