6ZL1 | pdb_00006zl1

Crystal structure of human serum albumin in complex with the MCL-1 neutralizing Alphabody CMPX-383B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 
    0.281 (Depositor), 0.312 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ZL1

This is version 1.2 of the entry. See complete history

Literature

Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting.

Pannecoucke, E.Van Trimpont, M.Desmet, J.Pieters, T.Reunes, L.Demoen, L.Vuylsteke, M.Loverix, S.Vandenbroucke, K.Alard, P.Henderikx, P.Deroo, S.Baatz, F.Lorent, E.Thiolloy, S.Somers, K.McGrath, Y.Van Vlierberghe, P.Lasters, I.Savvides, S.N.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abe1682
  • Primary Citation Related Structures: 
    6ZIE, 6ZL1

  • PubMed Abstract: 

    The therapeutic scope of antibody and nonantibody protein scaffolds is still prohibitively limited against intracellular drug targets. Here, we demonstrate that the Alphabody scaffold can be engineered into a cell-penetrating protein antagonist against induced myeloid leukemia cell differentiation protein MCL-1, an intracellular target in cancer, by grafting the critical B-cell lymphoma 2 homology 3 helix of MCL-1 onto the Alphabody and tagging the scaffold's termini with designed cell-penetration polypeptides. Introduction of an albumin-binding moiety extended the serum half-life of the engineered Alphabody to therapeutically relevant levels, and administration thereof in mouse tumor xenografts based on myeloma cell lines reduced tumor burden. Crystal structures of such a designed Alphabody in complex with MCL-1 and serum albumin provided the structural blueprint of the applied design principles. Collectively, we provide proof of concept for the use of Alphabodies against intracellular disease mediators, which, to date, have remained in the realm of small-molecule therapeutics.


  • Organizational Affiliation
    • VIB Center for Inflammation Research, 9052 Ghent, Belgium.

Macromolecule Content 

  • Total Structure Weight: 168.64 kDa 
  • Atom Count: 8,860 
  • Modeled Residue Count: 1,339 
  • Deposited Residue Count: 1,504 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Albumin
A, B
609Homo sapiensMutation(s): 0 
Gene Names: ALBGIG20GIG42PRO0903PRO1708PRO2044PRO2619PRO2675UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens)
Explore P02768 
Go to UniProtKB:  P02768
PHAROS:  P02768
GTEx:  ENSG00000163631 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CMPX-383B
C, D
143synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free:  0.281 (Depositor), 0.312 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.688α = 90
b = 231.346β = 90
c = 240.191γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary