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 

wwPDB Validation 3D Report Full Report


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 ...

    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 1AB491Megathura crenulataMutation(s): 0 
Gene Names: KLH1
Find proteins for Q10583 (Megathura crenulata)
Explore Q10583 
Go to UniProtKB:  Q10583
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
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 

  • 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