Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 209.48 kDa 
• Atom Count: 14847 
• Residue Count: 1743 
• Unique protein chains: 4

1X9F

Hemoglobin Dodecamer from Lumbricus Erythrocruorin

• DOI: 10.2210/pdb1X9F/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Lumbricus terrestris
• Mutation(s): No 


• Deposited: 2004-08-20 Released: 2004-11-30 
• Deposition Author(s): Strand, K., Knapp, J.E., Bhyravbhatla, B., Royer Jr., W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.246 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

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

• PubMed: 15504406 
• DOI: 10.1016/j.jmb.2004.08.094
• Primary Citation of Related Structures:  
  1X9F


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Globin IV, extracellular	A, E, I	151	Lumbricus terrestris	Mutation(s): 0
Find proteins for P13579 (Lumbricus terrestris) Explore P13579  Go to UniProtKB:  P13579

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Globin II, extracellular	B, F, J	145	Lumbricus terrestris	Mutation(s): 0
Find proteins for P02218 (Lumbricus terrestris) Explore P02218  Go to UniProtKB:  P02218

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Globin III, extracellular	C, G, K	153	Lumbricus terrestris	Mutation(s): 0
Find proteins for P11069 (Lumbricus terrestris) Explore P11069  Go to UniProtKB:  P11069

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
hemoglobin chain d1	D, H, L	140	Lumbricus terrestris	Mutation(s): 0
Find proteins for O61233 (Lumbricus terrestris) Explore O61233  Go to UniProtKB:  O61233

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B, C, D, E, F, G, H, I, J, K, L	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PO4	C, G, K	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CMO	A, B, C, D, E, F, G, H, I, J, K, L	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.246 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.225	α = 90
b = 172.071	β = 90
c = 202.886	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-20 
• Released Date: 2004-11-30 
Deposition Author(s): Strand, K., Knapp, J.E., Bhyravbhatla, B., Royer Jr., W.E.

Revision History 

• Version 1.0: 2004-11-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description