5F21

human CD38 in complex with nanobody MU375


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Immuno-targeting the multifunctional CD38 using nanobody

Li, T.Qi, S.Unger, M.Hou, Y.N.Deng, Q.W.Liu, J.Lam, C.M.Wang, X.W.Xin, D.Zhang, P.Koch-Nolte, F.Hao, Q.Zhang, H.Lee, H.C.Zhao, Y.J.

(2016) Sci Rep 6: 27055-27055

  • DOI: 10.1038/srep27055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CD38, as a cell surface antigen is highly expressed in several hematologic malignancies including multiple myeloma (MM) and has been proven to be a good target for immunotherapy of the disease. CD38 is also a signaling enzyme responsible for the meta ...

    CD38, as a cell surface antigen is highly expressed in several hematologic malignancies including multiple myeloma (MM) and has been proven to be a good target for immunotherapy of the disease. CD38 is also a signaling enzyme responsible for the metabolism of two novel calcium messenger molecules. To be able to target this multifunctional protein, we generated a series of nanobodies against CD38 with high affinities. Crystal structures of the complexes of CD38 with the nanobodies were solved, identifying three separate epitopes on the carboxyl domain. Chromobodies, engineered by tagging the nanobody with fluorescence proteins, provide fast, simple and versatile tools for quantifying CD38 expression. Results confirmed that CD38 was highly expressed in malignant MM cells compared with normal white blood cells. The immunotoxin constructed by splicing the nanobody with a bacterial toxin, PE38 shows highly selective cytotoxicity against patient-derived MM cells as well as the cell lines, with half maximal effective concentration reaching as low as 10(-11) molar. The effectiveness of the immunotoxin can be further increased by stimulating CD38 expression using retinoid acid. These results set the stage for the development of clinical therapeutics as well as diagnostic screening for myeloma.


    Organizational Affiliation

    School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
A
255Homo sapiensMutation(s): 5 
Gene Names: CD38
EC: 3.2.2.6
Find proteins for P28907 (Homo sapiens)
Go to Gene View: CD38
Go to UniProtKB:  P28907
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
nanobody MU375
B
156N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.149α = 90.00
b = 69.666β = 90.00
c = 123.476γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
REFMACrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-12-01 
  • Released Date: 2016-06-15 
  • Deposition Author(s): Hao, Q., Zhang, H.

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release