6UUP | pdb_00006uup

Structure of anti-hCD33 conditional scFv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.237 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.197 (Depositor) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6UUP

This is version 1.3 of the entry. See complete history

Literature

Direct control of CAR T cells through small molecule-regulated antibodies.

Park, S.Pascua, E.Lindquist, K.C.Kimberlin, C.Deng, X.Mak, Y.S.L.Melton, Z.Johnson, T.O.Lin, R.Boldajipour, B.Abraham, R.T.Pons, J.Sasu, B.J.Van Blarcom, T.J.Chaparro-Riggers, J.

(2021) Nat Commun 12: 710-710

  • DOI: https://doi.org/10.1038/s41467-020-20671-6
  • Primary Citation Related Structures: 
    6UUP, 6UY3

  • PubMed Abstract: 

    Antibody-based therapeutics have experienced a rapid growth in recent years and are now utilized in various modalities spanning from conventional antibodies, antibody-drug conjugates, bispecific antibodies to chimeric antigen receptor (CAR) T cells. Many next generation antibody therapeutics achieve enhanced potency but often increase the risk of adverse events. Antibody scaffolds capable of exhibiting inducible affinities could reduce the risk of adverse events by enabling a transient suspension of antibody activity. To demonstrate this, we develop conditionally activated, single-module CARs, in which tumor antigen recognition is directly modulated by an FDA-approved small molecule drug. The resulting CAR T cells demonstrate specific cytotoxicity of tumor cells comparable to that of traditional CARs, but the cytotoxicity is reversibly attenuated by the addition of the small molecule. The exogenous control of conditional CAR T cell activity allows continual modulation of therapeutic activity to improve the safety profile of CAR T cells across all disease indications.


  • Organizational Affiliation
    • Pfizer, La Jolla, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 116.52 kDa 
  • Atom Count: 7,645 
  • Modeled Residue Count: 911 
  • Deposited Residue Count: 1,084 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-CD33 conditional scFv
A, B, C, D
271Camelidae mixed libraryMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
DA [auth D],
EA [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG

Query on PEG



Download:Ideal Coordinates CCD File
AA [auth C],
IA [auth D],
M [auth A],
Q [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
FA [auth D]
G [auth A]
GA [auth D]
E [auth A],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
BA [auth C]
CA [auth C]
JA [auth D]
KA [auth D]
N [auth A]
BA [auth C],
CA [auth C],
JA [auth D],
KA [auth D],
N [auth A],
O [auth A],
R [auth B],
S [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.237 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.197 (Depositor) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.234α = 90
b = 104.635β = 113.572
c = 87.915γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary