8A9Q

Computational design of stable mammalian serum albumins for bacterial expression


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Stable Mammalian Serum Albumins Designed for Bacterial Expression.

Khersonsky, O.Goldsmith, M.Zaretsky, I.Hamer-Rogotner, S.Dym, O.Unger, T.Yona, M.Fridmann-Sirkis, Y.Fleishman, S.J.

(2023) J Mol Biol 435: 168191-168191

  • DOI: https://doi.org/10.1016/j.jmb.2023.168191
  • Primary Citation of Related Structures:  
    8A9Q

  • PubMed Abstract: 

    Albumin is the most abundant protein in the blood serum of mammals and has essential carrier and physiological roles. Albumins are also used in a wide variety of molecular and cellular experiments and in the cultivated meat industry. Despite their importance, however, albumins are challenging for heterologous expression in microbial hosts, likely due to 17 conserved intramolecular disulfide bonds. Therefore, albumins used in research and biotechnological applications either derive from animal serum, despite severe ethical and reproducibility concerns, or from recombinant expression in yeast or rice. We use the PROSS algorithm to stabilize human and bovine serum albumins, finding that all are highly expressed in E. coli. Design accuracy is verified by crystallographic analysis of a human albumin variant with 16 mutations. This albumin variant exhibits ligand binding properties similar to those of the wild type. Remarkably, a design with 73 mutations relative to human albumin exhibits over 40 °C improved stability and is stable beyond the boiling point of water. Our results suggest that proteins with many disulfide bridges have the potential to exhibit extreme stability when subjected to design. The designed albumins may be used to make economical, reproducible, and animal-free reagents for molecular and cell biology. They also open the way to high-throughput screening to study and enhance albumin carrier properties.


  • Organizational Affiliation

    Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel. Electronic address: [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Albumin
A, B
585Escherichia coliMutation(s): 16 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RWF (Subject of Investigation/LOI)
Query on RWF

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
R-WARFARIN
C19 H16 O4
PJVWKTKQMONHTI-OAHLLOKOSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth B]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
DAO
Query on DAO

Download Ideal Coordinates CCD File 
J [auth B]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RWF BindingDB:  8A9Q Kd: min: 2000, max: 5.10e+5 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.26α = 74.35
b = 92.128β = 89.29
c = 95.553γ = 79.98
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael1844/19
European Research Council (ERC)European Union815379

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2023-07-19
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection
  • Version 1.4: 2023-10-11
    Changes: Refinement description
  • Version 1.5: 2024-02-14
    Changes: Refinement description
  • Version 1.6: 2024-11-20
    Changes: Structure summary