1NOL

OXYGENATED HEMOCYANIN (SUBUNIT TYPE II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of deoxygenated Limulus polyphemus subunit II hemocyanin at 2.18 A resolution: clues for a mechanism for allosteric regulation.

Hazes, B.Magnus, K.A.Bonaventura, C.Bonaventura, J.Dauter, Z.Kalk, K.H.Hol, W.G.

(1993) Protein Sci 2: 597-619

  • DOI: 10.1002/pro.5560020411
  • Primary Citation of Related Structures:  
    1NOL, 1LLA

  • PubMed Abstract: 
  • The crystal structure of Limulus polyphemus subunit type II hemocyanin in the deoxygenated state has been determined to a resolution of 2.18 A. Phase information for this first structure of a cheliceratan hemocyanin was obtained by molecular replacem ...

    The crystal structure of Limulus polyphemus subunit type II hemocyanin in the deoxygenated state has been determined to a resolution of 2.18 A. Phase information for this first structure of a cheliceratan hemocyanin was obtained by molecular replacement using the crustacean hemocyanin structure of Panulirus interruptus. The most striking observation in the Limulus structure is the unexpectedly large distance of 4.6 A between both copper ions in the oxygen-binding site. Each copper has approximate trigonal planar coordination by three histidine N epsilon atoms. No bridging ligand between the copper ions could be detected. Other important new discoveries are (1) the presence of a cis-peptide bond between Glu 309 and Ser 310, with the carbonyl oxygen of the peptide plane hydrogen bonded to the N delta atom of the copper B ligand His 324; (2) localization of a chloride-binding site in the interface between the first and second domain; (3) localization of a putative calcium-binding site in the third domain. Furthermore, comparison of Limulus versus Panulirus hemocyanin revealed considerable tertiary and quaternary rigid body movements, although the overall folds are similar. Within the subunit, the first domain is rotated by about 7.5 degrees with respect to the other two domains, whereas within the hexamer the major movement is a 3.1 degrees rotation of the trimers with respect to each other. The rigid body rotation of the first domain suggests a structural mechanism for the allosteric regulation by chloride ions and probably causes the cooperative transition of the hexamer between low and high oxygen affinity states. In this postulated mechanism, the fully conserved Phe49 is the key residue that couples conformational changes of the dinuclear copper site into movements of the first domain.


    Related Citations: 
    • Crystal Structure of Hexameric Haemocyanin from Panulirus Interruptus Refined at 3.2 Angstroms Resolution
      Volbeda, A., Hol, W.G.J.
      (1989) J Mol Biol 209: 249
    • Structure of Hemocyanin II from the Horseshoe Crab, Limulus Polyphemus
      Nakashima, H., Behrens, P.Q., Moore, M.D., Yokota, E., Riggs, A.F.
      (1986) J Biol Chem 261: 10526

    Organizational Affiliation

    BIOSON Research Institute, Department of Chemistry, University of Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEMOCYANIN (SUBUNIT TYPE II)A628Limulus polyphemusMutation(s): 0 
Find proteins for P04253 (Limulus polyphemus)
Explore P04253 
Go to UniProtKB:  P04253
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PER
Query on PER

Download CCD File 
A
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: R 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.002α = 60.02
b = 117.002β = 60.02
c = 117.002γ = 60.02
Software Package:
Software NamePurpose
MADNES/KABSCHdata collection
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
KABSCHdata reduction
PROFILESdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1995-10-17 
  • Released Date: 1996-03-08 
  • Deposition Author(s): Hazes, B., Hol, W.G.J.

Revision History 

  • Version 1.0: 1996-03-08
    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