1LNL

Structure of deoxygenated hemocyanin from Rapana thomasiana

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

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This is version 1.5 of the entry. See complete history. 


Literature

The structure of a functional unit from the wall of a gastropod hemocyanin offers a possible mechanism for cooperativity

Perbandt, M., Guthoehrlein, E.W., Rypniewski, W., Idakieva, K., Stoeva, S., Voelter, W., Genov, N., Betzel, C.

(2003) Biochemistry 42: 6341-6346

  • DOI: 10.1021/bi020672x
  • Primary Citation of Related Structures:  
    1LNL

  • PubMed Abstract: 

    • Structure-function relationships in a molluscan hemocyanin have been investigated by determining the crystal structure of the Rapana thomasiana (gastropod) hemocyanin functional unit RtH2e in deoxygenated form at 3.38 A resolution. This is the first X-ra ...

    Structure-function relationships in a molluscan hemocyanin have been investigated by determining the crystal structure of the Rapana thomasiana (gastropod) hemocyanin functional unit RtH2e in deoxygenated form at 3.38 A resolution. This is the first X-ray structure of an unit from the wall of the molluscan hemocyanin cylinder. The crystal structure of RtH2e demonstrates molecular self-assembly of six identical molecules forming a regular hexameric cylinder. This suggests how the functional units are ordered in the wall of the native molluscan hemocyanins. The molecular arrangement is stabilized by specific protomer-to-protomer interactions, which are probably typical for the functional units building the wall of the cylinders. A molecular mechanism for cooperative dioxygen binding in molluscan hemocyanins is proposed on the basis of the molecular interactions between the protomers. In particular, the deoxygenated RtH2e structure reveals a tunnel leading from two opposite sides of the molecule to the active site. The tunnel represents a possible entrance pathway for dioxygen molecules. No such tunnels have been observed in the crystal structure of the oxy-Odg, a functional unit from the Octopus dofleini (cephalopod) hemocyanin in oxygenated form.

    Organizational Affiliation: 

    Institute of Biochemistry and Molecular Biology I, University Hospital Hamburg-Eppendorf, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hemocyanin A, B, C408Rapana venosaMutation(s): 0 
Find proteins for P83040 (Rapana venosa)
Explore P83040 
Go to UniProtKB:  P83040
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.486α = 90
b = 105.486β = 90
c = 374.988γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2018-07-04
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Advisory, Derived calculations
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary