3NP1

CRYSTAL STRUCTURE OF THE COMPLEX OF NITROPHORIN 1 FROM RHODNIUS PROLIXUS WITH CYANIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of a nitric oxide transport protein from a blood-sucking insect.

Weichsel, A.Andersen, J.F.Champagne, D.E.Walker, F.A.Montfort, W.R.

(1998) Nat.Struct.Mol.Biol. 5: 304-309

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The nitrophorins are heme-based proteins from the salivary glands of the blood-sucking insect Rhodnius prolixus that deliver nitric oxide gas (NO) to the victim while feeding, resulting in vasodilation and inhibition of platelet aggregation. The nitr ...

    The nitrophorins are heme-based proteins from the salivary glands of the blood-sucking insect Rhodnius prolixus that deliver nitric oxide gas (NO) to the victim while feeding, resulting in vasodilation and inhibition of platelet aggregation. The nitrophorins also bind tightly to histamine, which is released by the host to induce wound healing. Here we present three crystal structures of nitrophorin 1 (NP1): bound to cyanide, which binds in a manner similar to NO (2.3 A resolution); bound to histamine (2.0 A resolution); and bound to what appears to be NH3 from the crystallization solution (2.0 A resolution). The NP1 structures reveal heme to be sandwiched between strands of a lipocalin-like beta-barrel, and in an arrangement unlike any other gas-transport protein discovered to date. The heme is six-coordinate with a histidine (His 59) on the proximal side, and ligand in a spacious pocket on the distal side. The structures confirm that NO and histamine compete for the same binding pocket and become buried on binding. The dissociation constant for histamine binding was found to be 19 nM, approximately 100-fold lower than that for NO.


    Related Citations: 
    • Nitric Oxide Binding and Crystallization of Recombinant Nitrophorin I, a Nitric Oxide Transport Protein from the Blood-Sucking Bug Rhodnius Prolixus
      Andersen, J.F.,Champagne, D.E.,Weichsel, A.,Ribeiro, J.M.,Balfour, C.A.,Dress, V.,Montfort, W.R.
      (1997) Biochemistry 36: 4423


    Organizational Affiliation

    Department of Biochemistry, University of Arizona, Tucson 85721, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITROPHORIN 1
A, B
184Rhodnius prolixusMutation(s): 0 
Find proteins for Q26239 (Rhodnius prolixus)
Go to UniProtKB:  Q26239
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CYN
Query on CYN

Download SDF File 
Download CCD File 
A, B
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.390α = 90.00
b = 74.220β = 99.51
c = 66.230γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
AGROVATA/ROTAVATAdata reduction
X-PLORmodel building
X-PLORphasing
MADNESdata collection
ROTAVATAdata scaling
Agrovatadata scaling
MADNESdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-18
    Type: Data collection, Other, Refinement description