PDBsum entry: 2gtl

Oxygen storage/transport

PDB id: 2gtl

Contents

Protein chains

147 a.a. *

145 a.a. *

149 a.a. *

140 a.a. *

217 a.a. *

220 a.a. *

215 a.a. *

Ligands

CMO ×12

HEM ×12

Metals

_CA ×4

_ZN

* Residue conservation analysis

PDB id:

2gtl

Name:

Oxygen storage/transport

Title:

Lumbricus erythrocruorin at 3.5a resolution

Structure:

Extracellular globin 4. Chain: a, e, i. Synonym: globin iv, erythrocruorin, globin a. Extracellular globin 2. Chain: b, f, j. Synonym: globin ii, erythrocruorin, globin aiii, globin b. Extracellular globin-3. Chain: c, g, k. Synonym: extracellular globin iii, erythrocruorin, globin

Source:

Lumbricus terrestris. Common earthworm. Organism_taxid: 6398. Organism_taxid: 6398

Biol. unit:

240mer (from PDB file)

Resolution:

3.50Å R-factor: 0.288 R-free: 0.297

Authors:

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

Key ref:

W.E.Royer et al. (2006). Lumbricus erythrocruorin at 3.5 A resolution: architecture of a megadalton respiratory complex. Structure, 14, 1167-1177. PubMed id: 16843898 DOI: 10.1016/j.str.2006.05.011

Date:

28-Apr-06 Release date: 18-Jul-06

Protein chains

P13579  (GLB4_LUMTE) -  Extracellular globin-4

Seq: 151 a.a.

Struc: 147 a.a.*

Protein chains

P02218  (GLB2_LUMTE) -  Extracellular globin-2

Seq: 145 a.a.

Struc: 145 a.a.*

Protein chains

P11069  (GLB3_LUMTE) -  Extracellular globin-3

Seq: 170 a.a.

Struc: 149 a.a.*

Protein chains

O61233  (O61233_LUMTE) -  Hemoglobin chain d1 (Precursor)

Seq: 158 a.a.

Struc: 140 a.a.

Protein chain

Q9GV76  (Q9GV76_LUMTE) -  Hemoglobin linker chain L1

Seq: 240 a.a.

Struc: 217 a.a.

Protein chain

Q2I743  (Q2I743_LUMTE) -  Extracellular hemoglobin linker L2 subunit (Precursor)

Seq: 288 a.a.

Struc: 220 a.a.

Protein chain

Q2I742  (Q2I742_LUMTE) -  Extracellular hemoglobin linker L3 subunit (Precursor)

Seq: 240 a.a.

Struc: 215 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (2 terms)
• Biological process: transport (2 terms)
• Biochemical function: oxygen binding (5 terms)

DOI no: 10.1016/j.str.2006.05.011

Structure 14:1167-1177 (2006)

PubMed id: 16843898

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

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

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. 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.

Selected figure(s)

Figure 2.
Figure 2. Lumbricus Erythrocruorin Whole Molecule
(A) View along the molecular 6-fold axis. Hemoglobin subunits, at the outside of the molecule, are shown in a surface representation with a subunits in cyan, b subunits in dark yellow, c subunits in blue, and d subunits in dark purple. The course of polypeptide chains for linker subunits, in the interior of the molecule, is shown in red and gray for the two halves of the molecule.
(B) The whole molecule viewed along a P-dyad, rotated by 90° about the horizontal Q-dyad from the top view.
(C) Two one-twelfth units in the same orientation as in (B). Each one-twelfth unit includes a hemoglobin dodecamer and a linker heterotrimeric unit (red and gray). A local 3-fold relates three hemoglobin tetramers in the hemoglobin dodecamer and is coincident with a quasi-3-fold axis in the linker head region.

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 1167-1177) copyright 2006.

Figure was selected by the author.