2GTL

Lumbricus Erythrocruorin at 3.5A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.288 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Lumbricus erythrocruorin at 3.5 a resolution: architecture of a megadalton respiratory complex.

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

(2006) Structure 14: 1167-1177

  • DOI: 10.1016/j.str.2006.05.011
  • Primary Citation of Related Structures:  
    2GTL

  • PubMed Abstract: 
  • Annelid erythrocruorins are highly cooperative extracellular respiratory proteins with molecular masses on the order of 3.6 million Daltons. We report here the 3.5 A crystal structure of erythrocruorin from the earthworm Lumbricus terrestris. This structure reveals details of symmetrical and quasi-symmetrical interactions that dictate the self-limited assembly of 144 hemoglobin and 36 linker subunits ...

    Annelid erythrocruorins are highly cooperative extracellular respiratory proteins with molecular masses on the order of 3.6 million Daltons. We report here the 3.5 A crystal structure of erythrocruorin from the earthworm Lumbricus terrestris. This structure reveals details of symmetrical and quasi-symmetrical interactions that dictate the self-limited assembly of 144 hemoglobin and 36 linker subunits. The linker subunits assemble into a core complex with D(6) symmetry onto which 12 hemoglobin dodecamers bind to form the entire complex. Although the three unique linker subunits share structural similarity, their interactions with each other and the hemoglobin subunits display striking diversity. The observed diversity includes design features that have been incorporated into the linker subunits and may be critical for efficient assembly of large quantities of this complex respiratory protein.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA. william.royer@umassmed.edu



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular globin 4A, E, I151Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P13579 (Lumbricus terrestris)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular globin 2B, F, J145Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P02218 (Lumbricus terrestris)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular globin-3C, G, K153Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P11069 (Lumbricus terrestris)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin chain d1D, H, L140Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for O61233 (Lumbricus terrestris)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin linker chain L1M217Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q9GV76 (Lumbricus terrestris)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular hemoglobin linker L2 subunitN220Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q2I743 (Lumbricus terrestris)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular hemoglobin linker L3 subunitO215Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q2I742 (Lumbricus terrestris)
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth F] , CA [auth G] , EA [auth H] , GA [auth I] , IA [auth J] , KA [auth K] , MA [auth L] , Q [auth A] , 
AA [auth F],  CA [auth G],  EA [auth H],  GA [auth I],  IA [auth J],  KA [auth K],  MA [auth L],  Q [auth A],  S [auth B],  U [auth C],  W [auth D],  Y [auth E]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
PA [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
NA [auth M], OA [auth M], QA [auth N], RA [auth O]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CMO
Query on CMO

Download Ideal Coordinates CCD File 
BA [auth G] , DA [auth H] , FA [auth I] , HA [auth J] , JA [auth K] , LA [auth L] , P [auth A] , R [auth B] , 
BA [auth G],  DA [auth H],  FA [auth I],  HA [auth J],  JA [auth K],  LA [auth L],  P [auth A],  R [auth B],  T [auth C],  V [auth D],  X [auth E],  Z [auth F]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.288 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.08α = 89.69
b = 257.96β = 97.15
c = 436.53γ = 90.98
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance