1X9F

Hemoglobin Dodecamer from Lumbricus Erythrocruorin


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 

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Ligand Structure Quality Assessment 


This is version 1.4 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
  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Globin IV, extracellularA, E, I151Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P13579 (Lumbricus terrestris)
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Go to UniProtKB:  P13579
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UniProt GroupP13579
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Globin II, extracellularB, F, J145Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P02218 (Lumbricus terrestris)
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UniProt GroupP02218
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Globin III, extracellularC, G, K153Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P11069 (Lumbricus terrestris)
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Go to UniProtKB:  P11069
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UniProt GroupP11069
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
hemoglobin chain d1D, H, L140Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for O61233 (Lumbricus terrestris)
Explore O61233 
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UniProt GroupO61233
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
JA [auth K],
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
JA [auth K],
LA [auth L],
M [auth A],
O [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
IA [auth K],
Q [auth C],
Z [auth G]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CMO
Query on CMO

Download Ideal Coordinates CCD File 
BA [auth G],
DA [auth H],
FA [auth I],
HA [auth J],
KA [auth K],
BA [auth G],
DA [auth H],
FA [auth I],
HA [auth J],
KA [auth K],
MA [auth L],
N [auth A],
P [auth B],
S [auth C],
U [auth D],
W [auth E],
Y [auth F]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
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 = 139.225α = 90
b = 172.071β = 90
c = 202.886γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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