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- PDB-7f9w: CD25 in complex with Fab -

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Basic information

Entry
Database: PDB / ID: 7f9w
TitleCD25 in complex with Fab
Components
  • Heavy chain of Fab
  • Interleukin-2 receptor subunit alpha
  • Light chain of Fab
KeywordsANTITUMOR PROTEIN / CD25 / antibody / IL-2
Function / homology
Function and homology information


regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / activation-induced cell death of T cells / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / interleukin-2-mediated signaling pathway / activated T cell proliferation ...regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / activation-induced cell death of T cells / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / interleukin-2-mediated signaling pathway / activated T cell proliferation / inflammatory response to antigenic stimulus / Interleukin-2 signaling / positive regulation of T cell differentiation / positive regulation of activated T cell proliferation / Interleukin receptor SHC signaling / negative regulation of T cell proliferation / Notch signaling pathway / negative regulation of inflammatory response / RAF/MAP kinase cascade / cell surface receptor signaling pathway / immune response / inflammatory response / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Interleukin-2 receptor alpha / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-2 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu, C.
CitationJournal: Sci Rep / Year: 2021
Title: Two novel human anti-CD25 antibodies with antitumor activity inversely related to their affinity and in vitro activity.
Authors: Deyong Song / Xiu Liu / Chuangchuang Dong / Qiaoping Wang / Chunjie Sha / Chuan Liu / Zhenfei Ning / Jing Han / Hong Liu / Mengqi Zong / Yanyan Zhao / Ying Li / Guangsheng Liu / Xin Shao / Changlin Dou /
Abstract: High tumor regulatory T (Treg) cell infiltration is associated with poor prognosis of many cancers. CD25 is highly expressed on tumor Treg cells and is a potential target for Treg deletion. ...High tumor regulatory T (Treg) cell infiltration is associated with poor prognosis of many cancers. CD25 is highly expressed on tumor Treg cells and is a potential target for Treg deletion. Previously characterized anti-CD25 antibodies appear to have limited efficacy in tumor inhibition. Here we identified two human anti-CD25 antibodies, BA9 and BT942, which did not prevent the activation of IL-2R signaling pathway by IL-2. BT942 had weaker binding and cytotoxic activity to human CD25-expressing cell lines than BA9. But both demonstrated significant tumor growth inhibition in early and late-stage animal cancer models. BT942 resulted in a higher expansion of CD8 T cells and CD4 T cells in tumor microenvironment in mouse MC38 model compared to BA9. BT942 also demonstrated significant higher tumor growth inhibition and higher expansion of CD8 T cells and CD4 T cells in combination with an anti-PD1 antibody. Pharmacokinetic study of BT942 in cynomolgus monkeys demonstrated a half-life of 206.97 ± 19.03 h. Structural analysis by cryo-EM revealed that BT942 recognizes an epitope on opposite side of the CD25-IL-2 binding site, consistent with no IL-2 signaling blockade in vitro. BT942 appears to be an excellent candidate for cancer immunotherapy.
History
DepositionJul 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Interleukin-2 receptor subunit alpha
C: Light chain of Fab
B: Heavy chain of Fab


Theoretical massNumber of molelcules
Total (without water)92,1843
Polymers92,1843
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Interleukin-2 receptor subunit alpha / IL-2 receptor subunit alpha / IL-2-RA / IL-2R subunit alpha / IL2-RA / TAC antigen / p55


Mass: 18354.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RA / Production host: Homo sapiens (human) / References: UniProt: P01589
#2: Antibody Light chain of Fab


Mass: 24308.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Heavy chain of Fab


Mass: 49520.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1CD25 in complex with FabCOMPLEXFab fragment generated by proteolytic cleavage of IgG antibodyall0RECOMBINANT
2CD25COMPLEX#11RECOMBINANT
3FABCOMPLEX#2-#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Cricetulus griseus (Chinese hamster)10029
Buffer solutionpH: 7.4
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149373 / Symmetry type: POINT

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