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


Ligand Structure Quality Assessment 


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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular globin 4A, E, I151Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P13579 (Lumbricus terrestris)
Explore P13579 
Go to UniProtKB:  P13579
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13579
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular globin 2B, F, J145Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P02218 (Lumbricus terrestris)
Explore P02218 
Go to UniProtKB:  P02218
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02218
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular globin-3C, G, K153Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P11069 (Lumbricus terrestris)
Explore P11069 
Go to UniProtKB:  P11069
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11069
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin chain d1D, H, L140Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for O61233 (Lumbricus terrestris)
Explore O61233 
Go to UniProtKB:  O61233
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO61233
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin linker chain L1M217Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q9GV76 (Lumbricus terrestris)
Explore Q9GV76 
Go to UniProtKB:  Q9GV76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GV76
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular hemoglobin linker L2 subunitN220Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q2I743 (Lumbricus terrestris)
Explore Q2I743 
Go to UniProtKB:  Q2I743
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2I743
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular hemoglobin linker L3 subunitO215Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q2I742 (Lumbricus terrestris)
Explore Q2I742 
Go to UniProtKB:  Q2I742
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2I742
Protein Feature View
Expand
  • 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],
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],
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

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

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