3QJO

Refined Structure of the functional unit (KLH1-H) of keyhole limpet hemocyanin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 

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This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:3L6W


Literature

The refined structure of functional unit h of keyhole limpet hemocyanin (KLH1-h) reveals disulfide bridges.

Jaenicke, E.Buchler, K.Decker, H.Markl, J.Schroder, G.F.

(2011) IUBMB Life 63: 183-187

  • DOI: 10.1002/iub.435
  • Primary Citation of Related Structures:  
    3QJO

  • PubMed Abstract: 
  • Hemocyanins are multimeric oxygen-transport proteins in the hemolymph of many arthropods and mollusks. The overall molecular architecture of arthropod and molluscan hemocyanin is very different, although they possess a similar binuclear type 3 copper center to bind oxygen in a side-on conformation ...

    Hemocyanins are multimeric oxygen-transport proteins in the hemolymph of many arthropods and mollusks. The overall molecular architecture of arthropod and molluscan hemocyanin is very different, although they possess a similar binuclear type 3 copper center to bind oxygen in a side-on conformation. Gastropod hemocyanin is a 35 nm cylindrical didecamer (2 × 10-mer) based on a 400 kDa subunit. The latter is subdivided into eight paralogous "functional units" (FU-a to FU-h), each with an active site. FU-a to FU-f contribute to the cylinder wall, whereas FU-g and FU-h form the internal collar complex. Atomic structures of FU-e and FU-g, and a 9 Å cryoEM structure of the 8 MDa didecamer are available. Recently, the structure of keyhole limpet hemocyanin FU-h (KLH1-h) was presented as a C(α) -trace at 4 Å resolution. Unlike the other seven FU types, FU-h contains an additional C-terminal domain with a cupredoxin-like fold. Because of the resolution limit of 4 Å, in some loops, the course of the protein backbone could not be established with high certainty yet. Here, we present a refined atomic structure of FU-h (KLH1-h) obtained from low-resolution refinement, which unambiguously establishes the course of the polypeptide backbone and reveals the disulfide bridges as well as the orientation of bulky amino acids.


    Related Citations: 
    • Cupredoxin-like domains in haemocyanins.
      Jaenicke, E., Buchler, K., Markl, J., Decker, H., Barends, T.R.
      (2010) Biochem J 426: 373

    Organizational Affiliation

    Institut für Molekulare Biophysik, Johannes Gutenberg-Universität, Jakob Welder Weg 26, Mainz, Germany. elmar.jaenicke@uni-mainz.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemocyanin 1A, B491Megathura crenulataMutation(s): 0 
Gene Names: KLH1
UniProt
Find proteins for Q10583 (Megathura crenulata)
Explore Q10583 
Go to UniProtKB:  Q10583
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 251.02α = 90
b = 251.02β = 90
c = 251.02γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
RESOLVEmodel building
DMmodel building
CNSrefinement
XDSdata reduction
XSCALEdata scaling
RESOLVEphasing
DMphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description