2GTL

Lumbricus Erythrocruorin at 3.5A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.297 
  • R-Value Work: 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

  • 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 st ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Extracellular globin 4
A, E, I
151Lumbricus terrestrisN/A
Find proteins for P13579 (Lumbricus terrestris)
Go to UniProtKB:  P13579
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Extracellular globin 2
B, F, J
145Lumbricus terrestrisN/A
Find proteins for P02218 (Lumbricus terrestris)
Go to UniProtKB:  P02218
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Extracellular globin-3
C, G, K
153Lumbricus terrestrisN/A
Find proteins for P11069 (Lumbricus terrestris)
Go to UniProtKB:  P11069
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin chain d1
D, H, L
140Lumbricus terrestrisN/A
Find proteins for O61233 (Lumbricus terrestris)
Go to UniProtKB:  O61233
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin linker chain L1
M
217Lumbricus terrestrisN/A
Find proteins for Q9GV76 (Lumbricus terrestris)
Go to UniProtKB:  Q9GV76
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Extracellular hemoglobin linker L2 subunit
N
220Lumbricus terrestrisN/A
Find proteins for Q2I743 (Lumbricus terrestris)
Go to UniProtKB:  Q2I743
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Extracellular hemoglobin linker L3 subunit
O
215Lumbricus terrestrisN/A
Find proteins for Q2I742 (Lumbricus terrestris)
Go to UniProtKB:  Q2I742
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
M, N, O
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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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

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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: 3.5 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.288 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 176.080α = 89.69
b = 257.960β = 97.15
c = 436.530γ = 90.98
Software Package:
Software NamePurpose
ADSCdata collection
CNSphasing
PDB_EXTRACTdata extraction
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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