3NP1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


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 Biol 5: 304-309

  • DOI: 10.1038/nsb0498-304
  • Primary Citation of Related Structures:  
    1NP1, 2NP1, 3NP1

  • 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 nitrophorins also bind tightly to histamine, which is released by the host to induce wound healing ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NITROPHORIN 1A, B184Rhodnius prolixusMutation(s): 0 
UniProt
Find proteins for Q26239 (Rhodnius prolixus)
Explore Q26239 
Go to UniProtKB:  Q26239
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ26239
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CYN
Query on CYN

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.39α = 90
b = 74.22β = 99.51
c = 66.23γ = 90
Software Package:
Software NamePurpose
MADNESdata collection
AGROVATA/ROTAVATAdata reduction
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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