3QJO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.271 

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 - determined by Jaenicke, E., Buechler, K., Markl, J., Decker, H., Barends, T.R.M.  

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemocyanin 1
A, B
491Megathura crenulataMutation(s): 0 
Gene Names: KLH1
Find proteins for Q53IP9 (Megathura crenulata)
Go to UniProtKB:  Q53IP9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
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 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.271 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 251.020α = 90.00
b = 251.020β = 90.00
c = 251.020γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
DMphasing
MAR345data collection
CNSrefinement
RESOLVEphasing
XSCALEdata scaling
DMmodel building
RESOLVEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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