1X9F

Hemoglobin Dodecamer from Lumbricus Erythrocruorin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the hemoglobin dodecamer from lumbricus erythrocruorin: allosteric core of giant annelid respiratory complexes

Strand, K.Knapp, J.E.Bhyravbhatla, B.Royer Jr., W.E.

(2004) J.Mol.Biol. 344: 119-134

  • DOI: 10.1016/j.jmb.2004.08.094

  • PubMed Abstract: 
  • Erythrocruorins are highly cooperative giant extracellular respiratory complexes found in annelids, where they serve the same function as red blood cells. Our previous 5.5A resolution crystal structure of Lumbricus terrestris erythrocruorin revealed ...

    Erythrocruorins are highly cooperative giant extracellular respiratory complexes found in annelids, where they serve the same function as red blood cells. Our previous 5.5A resolution crystal structure of Lumbricus terrestris erythrocruorin revealed a hierarchical organization of 144 oxygen-binding hemoglobin chains that are assembled into 12 dodecamers arranged at the periphery of the complex around a central scaffold formed by 36 non-hemoglobin subunits. We present here the 2.6A resolution crystal structure of the Lumbricus hemoglobin dodecameric subassembly, which provides the first atomic models of the erythrocruorin allosteric core. The hemoglobin dodecamer has a molecular 3-fold axis of symmetry that relates three heterotetramers, each of which is composed of two tightly associated heterodimers. The structure reveals details of the interfaces, including key side-chain interactions likely to contribute to ligand-linked allosteric transitions, and shows the crowded nature of the ligand-binding pockets. Comparison of the Lumbricus dimeric assemblies with similar ones from mollusks and echinoderms suggests plausible pH-dependent quaternary transitions that may occur in response to proton binding and ligand release. Thus, these results provide the first step towards elucidating the structural basis for the strong allosteric properties of Lumbricus erythrocruorin.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, LRB 921, 364 Plantation Street, Worcester, MA 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Globin IV, extracellular
A, E, I
151Lumbricus terrestrisMutation(s): 0 
Find proteins for P13579 (Lumbricus terrestris)
Go to UniProtKB:  P13579
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Globin II, extracellular
B, F, J
145Lumbricus terrestrisMutation(s): 0 
Find proteins for P02218 (Lumbricus terrestris)
Go to UniProtKB:  P02218
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Globin III, extracellular
C, G, K
153Lumbricus terrestrisMutation(s): 0 
Find proteins for P11069 (Lumbricus terrestris)
Go to UniProtKB:  P11069
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
hemoglobin chain d1
D, H, L
140Lumbricus terrestrisMutation(s): 0 
Find proteins for O61233 (Lumbricus terrestris)
Go to UniProtKB:  O61233
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C, G, K
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 139.225α = 90.00
b = 172.071β = 90.00
c = 202.886γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description