4B3W

Crystal structure of human cytoglobin H(E7)Q mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Co Rebinding Kinetics and Molecular Dynamics Simulations Highlight Dynamic Regulation of Internal Cavities in Human Cytoglobin.

Gabba, M.Abbruzzetti, S.Spyrakis, F.Forti, F.Bruno, S.Mozzarelli, A.Luque, F.J.Viappiani, C.Cozzini, P.Nardini, M.Germani, F.Bolognesi, M.Moens, L.Dewilde, S.

(2013) Plos One 8: 49770

  • DOI: 10.1371/journal.pone.0049770

  • PubMed Abstract: 
  • Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes ...

    Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation) of a bis-histidyl heme hexacoordinated reaction intermediate. Ligand exit to the solvent occurs through distinct pathways, some of which exploit temporary docking sites. The remarkable change in energetic barriers, linked to heme bis-histidyl hexacoordination by HisE7, may be responsible for active regulation of the flux of reactants and products to and from the reaction site on the distal side of the heme. A substantial change in both protein dynamics and inner cavities is observed upon transition from the CO-liganded to the pentacoordinated and bis-histidyl hexacoordinated species, which could be exploited as a signalling state. These findings are consistent with the expected versatility of the molecular activity of this protein.


    Organizational Affiliation

    Institute of Complex Systems - Molekulare Biophysik (ICS-5) Forschungszentrum Jülich, Jülich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOGLOBIN
A, B
190Homo sapiensMutation(s): 3 
Gene Names: CYGB (STAP)
Find proteins for Q8WWM9 (Homo sapiens)
Go to Gene View: CYGB
Go to UniProtKB:  Q8WWM9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FC6
Query on FC6

Download SDF File 
Download CCD File 
A, B
HEXACYANOFERRATE(3-)
FERRI(III)HEXACYANIDE
C6 Fe N6
HCMVSLMENOCDCK-UHFFFAOYSA-N
 Ligand Interaction
CYN
Query on CYN

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

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 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: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.844α = 90.00
b = 70.054β = 90.00
c = 102.072γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release