Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18200.65 
• Atom Count: 1279 
• Residue Count: 158 
• Unique protein chains: 1

1HLB

Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola

• DOI: 10.2210/pdb1HLB/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Molpadia arenicola


• Deposited: 1994-03-22 Released: 1994-06-22 
• Deposition Author(s): Hackert, M.L., Mitchell, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Work: 0.150 

Literature

Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola.

Mitchell, D.T., Kitto, G.B., Hackert, M.L.

(1995) J.Mol.Biol. 251: 421-431

• PubMed: 7650740 


• PubMed Abstract: 
  

The X-ray structures of two hemoglobins (Hb) from the sea cucumber Caudina arenicola (an echinoderm) have been determined: a low spin, hemichrome, monomeric Hb-C chain, and a cyanomet-liganded dimeric Hb-D chain. Attempts to obtain crystal structures of the deoxy-liganded and hemichrome forms from the same chain type have not been successful. In this work, the Hb-C chain and Hb-D chain structures are compared, and differences observed in tertiary structure related to the different ligand states for hemoglobin chains from this organism. In addition to shifts of the distal histidine and E helix, differences are noted in the position of the heme group within the heme pocket, the hydrogen bonding of the heme group to the protein, and the status of the D helix. These differences are important in understanding the ligand-linked association states of these hemoglobins. The quaternary structure of the Hb-D homodimer is compared with those from two other invertebrate hemoglobins from Scapharca inaequivalvis and Urechis caupo, which also have subunit-subunit interactions that involve the E and E' helices. The dimer interactions of the Caudina and Urechis hemoglobins are quite dissimilar. However, the dimer interface observed in cyanomet Hb-D is strikingly similar to that observed for the carbonmonoxy hemoglobin dimer from the clam, Scapharca, yet many of the key amino acid residues implicated in the cooperative mechanism of the Scapharca hemoglobin are not conserved in the Caudina hemoglobins.

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Related Citations: 

• Amino Acid Sequence of the Coelomic C Globin from the Sea Cucumber Caudina (Molpadia) Arenicola
  Mcdonald, G.D.,Davidson, L.,Kitto, G.B.
  (1992) J.Protein Chem. 11: 29
• Preliminary Crystallographic Data on Monomeric and Dimeric Hemoglobins from the Sea Cucumber, Molpadia Arenicola
  Carson, W.M.,Bowers, T.R.,Kitto, G.B.,Hackert, M.L.
  (1979) J.Biol.Chem. 254: 7400
• Functional Consequences of Ligand-Linked Dissociation in Hemoglobin from the Sea Cucumber Molpadia Arenicola
  Bonaventura, C.,Bonaventura, J.,Kitto, B.,Brunori, M.,Antonini, E.
  (1976) Biochim.Biophys.Acta 428: 779
• N-Terminal Substitution of Some Sea Cucumber Hemoglobins
  Kitto, G.B.,Erwin, D.,West, R.,Omnaas, J.
  (1976) COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. 55: 105




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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Texas at Austin 78712, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HEMOGLOBIN (DEOXY)	A	158	Molpadia arenicola	Mutation(s): 0
Find proteins for P80018 (Molpadia arenicola) Go to UniProtKB:  P80018

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ACE	A	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Work: 0.150 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 45.740	α = 90.00
b = 45.230	β = 104.40
c = 40.920	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
X-PLOR	model building
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-03-22 
• Released Date: 1994-06-22 
• Deposition Author(s): Hackert, M.L., Mitchell, D.T.

Revision History 

• Version 1.0: 1994-06-22
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-11-29
  Type: Derived calculations, Other