1UMO

The crystal structure of cytoglobin: the fourth globin type discovered in man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of cytoglobin: the fourth globin type discovered in man displays heme hexa-coordination.

de Sanctis, D.Dewilde, S.Pesce, A.Moens, L.Ascenzi, P.Hankeln, T.Burmester, T.Bolognesi, M.

(2004) J Mol Biol 336: 917-927

  • DOI: 10.1016/j.jmb.2003.12.063
  • Primary Citation of Related Structures:  
    1UMO, 1URV, 1UT0

  • PubMed Abstract: 
  • Cytoglobin is a recently discovered hemeprotein belonging to the globin superfamily together with hemoglobin, myoglobin and neuroglobin. Although distributed in almost all human tissues, cytoglobin has not been ascribed a specific function. Human cyt ...

    Cytoglobin is a recently discovered hemeprotein belonging to the globin superfamily together with hemoglobin, myoglobin and neuroglobin. Although distributed in almost all human tissues, cytoglobin has not been ascribed a specific function. Human cytoglobin is composed of 190 amino acid residues. Sequence alignments show that a protein core region (about 150 residues) is structurally related to hemoglobin and myoglobin, being complemented by about 20 extra residues both on the N and C termini. In the absence of exogenous ligands (e.g. O2), the cytoglobin distal HisE7 residue is coordinated to the heme Fe atom, thus decreasing the ligand affinity. The crystal structure of human cytoglobin (2.1 A resolution, 21.3% R-factor) highlights a three-over-three alpha-helical globin fold, covering residues 18-171; the 1-17 N-terminal, and the 172-190 C-terminal residue segments are disordered in both molecules of the crystal asymmetric unit. Heme hexa-coordination is evident in one of the two cytoglobin chains, whereas alternate conformation for the heme distal region, achieving partial heme penta-coordination, is observed in the other. Human cytoglobin displays a large apolar protein matrix cavity, next to the heme, not related to the myoglobin cavities recognized as temporary ligand docking stations. The cavity, which may provide a heme ligand diffusion pathway, is connected to the external space through a narrow tunnel nestled between the globin G and H helices.


    Organizational Affiliation

    Department of Physics-INFM, Centre for Excellence in Biomedical Research, University of Genova, Via Dodecaneso 33, 1-16146 Genova, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOGLOBINAB190Homo sapiensMutation(s): 2 
Gene Names: CYGBSTAP
Find proteins for Q8WWM9 (Homo sapiens)
Explore Q8WWM9 
Go to UniProtKB:  Q8WWM9
NIH Common Fund Data Resources
PHAROS  Q8WWM9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.617α = 90
b = 72.001β = 90
c = 98.334γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-06-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2019-10-09
    Changes: Data collection, Database references, Other