8WZS | pdb_00008wzs

Crystal structure of SRCRD11 of human DMBT1 from needle-shape crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 
    0.243 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8WZS

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Literature

Refolding, Crystallization, and Crystal Structure Analysis of a Scavenger Receptor Cysteine-Rich Domain of Human Salivary Agglutinin Expressed in Escherichia coli.

Zhang, C.Lu, P.Wei, S.Hu, C.Miyoshi, M.Okamoto, K.Itoh, H.Okuda, S.Suzuki, M.Kawakami, H.Nagata, K.

(2024) Protein J 43: 283-297

  • DOI: https://doi.org/10.1007/s10930-023-10173-x
  • Primary Citation Related Structures: 
    8J8D, 8WZS

  • PubMed Abstract: 

    Scavenger receptors are a protein superfamily that typically consists of one or more repeats of the scavenger receptor cysteine-rich structural domain (SRCRD), which is an ancient and highly conserved protein module. The expression and purification of eukaryotic proteins containing multiple disulfide bonds has always been challenging. The expression systems that are commonly used to express SRCRD proteins mainly consist of eukaryotic protein expression systems. Herein, we established a high-level expression strategy of a Type B SRCRD unit from human salivary agglutinin using the Escherichia coli expression system, followed by a refolding and purification process. The untagged recombinant SRCRD was expressed in E. coli using the pET-32a vector, which was followed by a refolding process using the GSH/GSSG redox system. The SRCRD expressed in E. coli SHuffle T7 showed better solubility after refolding than that expressed in E. coli BL21(DE3), suggesting the importance of the disulfide bond content prior to refolding. The quality of the refolded protein was finally assessed using crystallization and crystal structure analysis. As proteins refolded from inclusion bodies exhibit a high crystal quality and reproducibility, this method is considered a reliable strategy for SRCRD protein expression and purification. To further confirm the structural integrity of the refolded SRCRD protein, the purified protein was subjected to crystallization using sitting-drop vapor diffusion method. The obtained crystals of SRCRD diffracted X-rays to a resolution of 1.47 Å. The solved crystal structure appeared to be highly conserved, with four disulfide bonds appropriately formed. The surface charge distribution of homologous SRCRD proteins indicates that the negatively charged region at the surface is associated with their calcium-dependent ligand recognition. These results suggest that a high-quality SRCRD protein expressed by E. coli SHuffle T7 can be successfully folded and purified, providing new options for the expression of members of the scavenger receptor superfamily.


  • Organizational Affiliation
    • Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Macromolecule Content 

  • Total Structure Weight: 12.68 kDa 
  • Atom Count: 890 
  • Modeled Residue Count: 107 
  • Deposited Residue Count: 119 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Deleted in malignant brain tumors 1 protein119Homo sapiensMutation(s): 0 
Gene Names: DMBT1GP340
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGM3 (Homo sapiens)
Explore Q9UGM3 
Go to UniProtKB:  Q9UGM3
PHAROS:  Q9UGM3
GTEx:  ENSG00000187908 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGM3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free:  0.243 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.114α = 90
b = 71.114β = 90
c = 55.387γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP18H02151

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release