7RBW | pdb_00007rbw

Structure of Biliverdin-binding Serpin of Boana punctata (polka-dot tree frog)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.237 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural and Functional Characterization of a Biliverdin-Binding Near-Infrared Fluorescent Protein From the Serpin Superfamily.

Manoilov, K.Y.Ghosh, A.Almo, S.C.Verkhusha, V.V.

(2021) J Mol Biology 434: 167359-167359

  • DOI: https://doi.org/10.1016/j.jmb.2021.167359
  • Primary Citation Related Structures: 
    7RBW

  • PubMed Abstract: 

    Biliverdin-binding serpins (BBSs) are proteins that are responsible for coloration in amphibians and fluoresce in the near-infrared (NIR) spectral region. Here we produced the first functional recombinant BBS of the polka-dot treefrog Boana punctata (BpBBS), assembled with its biliverdin (BV) chromophore, and report its biochemical and photochemical characterization. We determined the crystal structure of BpBBS at 2.05 Å resolution, which demonstrated its structural homology to the mammalian protease inhibitor alpha-1-antitrypsin. BV interaction with BpBBS was studied and it was found that the N-terminal polypeptide (residues 19-50) plays a critical role in the BV binding. By comparing BpBBS with the available NIR fluorescent proteins and expressing it in mammalian cells, we demonstrated its potential as a NIR imaging probe. These results provide insight into the non-inhibitory function of serpins, provide a basis for improving their performance in mammalian cells, and suggest possible paths for the development of BBS-based fluorescent probes.


  • Organizational Affiliation
    • Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Macromolecule Content 

  • Total Structure Weight: 95.82 kDa 
  • Atom Count: 6,390 
  • Modeled Residue Count: 760 
  • Deposited Residue Count: 822 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Biliverdin bindin serpin
A, B
411Boana punctataMutation(s): 0 
Gene Names: BBS
UniProt
Find proteins for A0A7D7FB99 (Boana punctata)
Explore A0A7D7FB99 
Go to UniProtKB:  A0A7D7FB99
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7D7FB99
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.237 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.069α = 90
b = 75.91β = 90
c = 143.751γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R35GM122567

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2021-12-08
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description