1HCY

CRYSTAL STRUCTURE OF HEXAMERIC HAEMOCYANIN FROM PANULIRUS INTERRUPTUS REFINED AT 3.2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of hexameric haemocyanin from Panulirus interruptus refined at 3.2 A resolution.

Volbeda, A.Hol, W.G.

(1989) J Mol Biol 209: 249-279

  • DOI: 10.1016/0022-2836(89)90276-3
  • Primary Citation of Related Structures:  
    1HC1, 1HCY

  • PubMed Abstract: 
  • The use of non-crystallographic symmetry restraints in the refinement of the haemocyanin hexamer from Panulirus interruptus at 3.2 A resolution has resulted in a final model with a very reasonable geometry and a crystallographic R-factor of 20.1%, us ...

    The use of non-crystallographic symmetry restraints in the refinement of the haemocyanin hexamer from Panulirus interruptus at 3.2 A resolution has resulted in a final model with a very reasonable geometry and a crystallographic R-factor of 20.1%, using 59,193 observed structure factor amplitudes between 8.0 and 3.2 A. The mean co-ordinate error is approximately 0.35 A. The six subunits appear to be related by symmetry operations that differ slightly from 32 point group symmetry. The six subunits have essentially maintained the same structure. The hexamer, with point group 32, is best described as a trimer of "tight dimers". The contacts between the subunits in such a dimer are more numerous, and better conserved during evolution than contacts in a trimer. The interface of a tight dimer is separated by an internal cavity into two "contact areas". The contact area nearest to the centre of the hexamer is most extensive and consists mainly of residues that are quite conserved among arthropodan haemocyanins. All these residues are provided by the second domain of each subunit. Hence, this second domain may play a crucial role in the allosteric functioning of this oxygen transport protein. The dinuclear copper oxygen-binding site resides in the centre of domain 2. This oxygen-binding centre is not fully accessible from the solvent. Three large cavities occur, however, within each subunit at the interfaces of the three domains. All three cavities contain ordered water molecules, and two of them are accessible from the surrounding solvent. These cavities may play a role in facilitating fast movement of dioxygen towards the binding site, which is situated in a highly conserved, rather hydrophobic core. A detailed definition of the geometry of the copper site is, of course, not possible at the limited resolution of 3.2 A. Nevertheless, it is possible to conclude that each copper is co-ordinated by two, more or less tightly bound, histidine ligands and one more distant histidine residue. The six histidine residues utilize their N epsilon atoms for copper co-ordination, while their N delta atoms are engaged in hydrogen bonds with conserved residues or water molecules. The two distant histidine ligands are located in apical positions and are on opposite sides with respect to the plane approximately defined by the four more tightly bound histidine ligands and the two copper ions. The copper-to-copper distance is 3.5 to 3.6 A in four of the subunits, but this distance deviates considerably in two others.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Spectroscopic Investigations of Panulirus Interruptus Hemocyanin in the Crystalline State
      Volbeda, A., Feiters, M.C., Vincent, M.G., Bouwman, E., Dobson, B., Kalk, K.H., Reedijk, J., Hol, W.G.J.
      (1989) Eur J Biochem 181: 669
    • Pseudo 2-Fold Symmetry in the Copper-Binding Domain of Arthropodan Haemocyanins. Possible Implications for the Evolution of Oxygen Transport Proteins
      Volbeda, A., Hol, W.G.J.
      (1989) J Mol Biol 206: 531
    • Panulirus Interruptus Hemocyanin. The Amino Acid Sequence of Subunit B and Anomalous Behavior of Subunits a and B on Polyacrylamide Gel Electrophoresis in the Presence of /Sds
      Jekel, P.A., Bak, H.J., Soeter, N.M., Vereijken, J.M., Beintema, J.J.
      (1988) Eur J Biochem 178: 403
    • Panulirus Interruptus Hemocyanin. The Elucidation of the Complete Amino Acid Sequence of Subunit A
      Bak, H.J., Beintema, J.J.
      (1987) Eur J Biochem 169: 333
    • Structure Determination of Panulirus Interruptus Haemocyanin at 3.2 Angstroms Resolution. Successful Phase Extension by Sixfold Density Averaging
      Gaykema, W.P.J., Volbeda, A., Hol, W.G.J.
      (1986) J Mol Biol 187: 255
    • The Structure of Arthropod Hemocyanins
      Linzen, B., Soeter, N.M., Riggs, A.F., Schneider, H.-J., Schartau, W., Moore, M.D., Yokota, E., Behrens, P.Q., Nakashima, H., Takagi, T., Nemoto, T., Vereijken, J.M., Bak, H.J., Beintema, J.J., Volbeda, A., Gaykema, W.P.J., Hol, W.G.J.
      (1985) Science 229: 519
    • 3.2 Angstroms Structure of the Copper-Containing, Oxygen-Carrying Protein Panulirus Interruptus Haemocyanin
      Gaykema, W.P.J., Hol, W.G.J., Vereijken, J.M., Soeter, N.M., Bak, H.J., Beintema, J.J.
      (1984) Nature 309: 23

    Organizational Affiliation

    Department of Chemistry, University of Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ARTHROPODAN HEMOCYANINABCDEF657Panulirus interruptusMutation(s): 0 
Find proteins for P04254 (Panulirus interruptus)
Explore P04254 
Go to UniProtKB:  P04254
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, K, L
2 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

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A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.8α = 90
b = 193.1β = 118.1
c = 122.2γ = 90
Software Package:
Software NamePurpose
CORELSrefinement
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary