3PUB | pdb_00003pub

Crystal structure of the Bombyx mori low molecular weight lipoprotein 7 (Bmlp7)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.235 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the 30 K protein from the silkworm Bombyx mori reveals a new member of the beta-trefoil superfamily

Yang, J.-P.Ma, X.-X.He, Y.-X.Li, W.-F.Kang, Y.Bao, R.Chen, Y.Zhou, C.-Z.

(2011) J Struct Biol 175: 97-103

  • DOI: https://doi.org/10.1016/j.jsb.2011.04.003
  • Primary Citation Related Structures: 
    3PUB

  • PubMed Abstract: 

    The hemolymph of the fifth instar larvae of the silkworm Bombyx mori contains a group of homologous proteins with a molecular weight of approximately 30 kDa, termed B. mori low molecular weight lipoproteins (Bmlps), which account for about 5% of the total plasma proteins. These so-called "30 K proteins" have been reported to be involved in the innate immune response and transportation of lipid and/or sugar. To elucidate their molecular functions, we determined the crystal structure of a 30 K protein, Bmlp7, at 1.91Å. It has two distinct domains: an all-α N-terminal domain (NTD) and an all-β C-terminal domain (CTD) of the β-trefoil fold. Comparative structural analysis indicates that Bmlp7 represents a new family, adding to the 14 families currently identified, of the β-trefoil superfamily. Structural comparison and simulation suggest that the NTD has a putative lipid-binding cavity, whereas the CTD has a potential sugar-binding site. However, we were unable to detect the binding of either lipid or sugar. Therefore, further investigations are needed to characterize the molecular function of this protein.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 57.93 kDa 
  • Atom Count: 3,932 
  • Modeled Residue Count: 471 
  • Deposited Residue Count: 502 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
30kDa protein
A, B
251Bombyx moriMutation(s): 0 
UniProt
Find proteins for E5EVW2 (Bombyx mori)
Explore E5EVW2 
Go to UniProtKB:  E5EVW2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5EVW2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.235 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.855α = 93.26
b = 49.322β = 94.04
c = 54.79γ = 103.47
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-03-05
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references