Structural characterization of the hexa-coordinated globin from Spisula solidissima

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


Structural and dynamic characterization of the hexa-coordinated globin from Spisula solidissima.

Pesce, A.Barmpidi, K.Dewilde, S.Estarellas, C.Moens, L.Bolognesi, M.Luque, F.J.Nardini, M.

(2023) J Inorg Biochem 246: 112289-112289

  • DOI: https://doi.org/10.1016/j.jinorgbio.2023.112289
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    High energy consumption in the nervous system requires a continuous supply of O 2 . This role is assisted by proteins from the globin super-family in the nerve cells of invertebrates, where 'nerve hemoglobins' (nHbs) are mainly present at mM concentrations and exhibit oxygen affinities comparable to those of vertebrate myoglobins. To gain insight into the structural bases of this function, we report the crystal structure of nHb from the Atlantic surf clam Spisula solidissima (SsHb), previously suggested to display a bis-histidyl hexa-coordinated heme in the deoxy state, high O 2 affinity, and ligand binding cooperativity when assayed in situ. The crystallized protein forms a dimer through packing of a 4-helix bundle involving helices E and F of each subunit. The SsHb 'classic' globin fold displays bis-histidyl (His71(E7) and His103(F8)) hexa-coordination of the heme-Fe atom, with structural and dynamics variations found in the inter-helix hinge regions. Molecular Dynamics simulations of both monomeric and dimeric species in the bis-histidyl hexa-coordinated, deoxy penta-coordinated, and O 2 -bound hexa-coordinated states reveal distinct structural rearrangements at the interface between subunits in the dimer; these would affect the magnitude of the conformational fluctuations observed between monomer and dimer, and the topology of cavities within the protein matrix and at the interface. These results point to a distal site opening mechanism allowing access of the exogenous ligand to the heme and cast hypotheses on the dimer interface structural and dynamic properties that may support ligand binding cooperativity in dimeric SsHb.

  • Organizational Affiliation

    Department of Physics, University of Genova, Via Dodecaneso 33, I-16146 Genova, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nerve hemoglobin
A, B, C, D
162Spisula solidissimaMutation(s): 0 
Gene Names: nHb
Find proteins for Q3MQ26 (Spisula solidissima)
Explore Q3MQ26 
Go to UniProtKB:  Q3MQ26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3MQ26
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.219α = 75.65
b = 50.684β = 88.09
c = 74.165γ = 85.3
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-117646RB-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainCEX2021-001202-M

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release