1X8P

0.85 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Complexed With Ammonia at pH 7.4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Protein functional cycle viewed at atomic resolution: conformational change and mobility in nitrophorin 4 as a function of pH and NO binding

Kondrashov, D.A.Roberts, S.A.Weichsel, A.Montfort, W.R.

(2004) Biochemistry 43: 13637-13647

  • DOI: 10.1021/bi0483155
  • Primary Citation of Related Structures:  1X8N, 1X8O, 1X8Q

  • PubMed Abstract: 
  • The blood-sucking insect Rhodnius prolixus uses nitrophorin 4, a heme protein, to deliver nitric oxide (NO) to a victim, causing vasodilation and improved feeding. Binding of NO occurs at a ferric heme and is modulated by pH. NO binding at lower pH i ...

    The blood-sucking insect Rhodnius prolixus uses nitrophorin 4, a heme protein, to deliver nitric oxide (NO) to a victim, causing vasodilation and improved feeding. Binding of NO occurs at a ferric heme and is modulated by pH. NO binding at lower pH induces a large conformational change involving loops A-B and G-H that leads to distal pocket desolvation and protection of the nitrosyl heme complex. We have determined the crystal structures of Rhodnius nitrophorin 4 to ultrahigh resolution in four functional states: +/-NO at pH = 7.4 and +/-NO at pH = 5.6. The structure with NO at pH 7.4 (1.08 A) is newly determined while the other complexes have been modeled to resolutions much greater than previously reported (1.0-0.85 A). The ultrahigh resolution allowed us to resolve multiple conformers in binding-site loops, leading to a detailed description of the dynamics involved with storing NO in the insect salivary gland at low pH, and releasing NO in response to the increased pH of a victim's tissue. Strikingly, features for both the "open" and "closed" conformers exist under all conditions, suggesting that the flexible loops can transition with relative ease between conformational states. Yet, release of NO from rNP4 is much slower than found for other ferric heme proteins. The structures suggest that highly mobile loops can limit diffusion of diatomic molecules into and out of a protein cavity, a result with implications for the role of protein dynamics in function.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biophysics and Program in Applied Mathematics, University of Arizona, Tucson, Arizona 85721, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrophorin 4
A
184Rhodnius prolixusEC: 1.7.6.1
Find proteins for Q94734 (Rhodnius prolixus)
Go to UniProtKB:  Q94734
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NH3
Query on NH3

Download SDF File 
Download CCD File 
A
AMMONIA
H3 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.131 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.320α = 90.00
b = 42.810β = 94.10
c = 52.920γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
SHELXphasing
SHELXL-97refinement
SHELXmodel building
d*TREKdata reduction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance