2D2M

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.

Numoto, N.Nakagawa, T.Kita, A.Sasayama, Y.Fukumori, Y.Miki, K.

(2005) Proc.Natl.Acad.Sci.USA 102: 14521-14526

  • DOI: 10.1073/pnas.0501541102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports ...

    Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports oxygen and sulfide simultaneously. The symbiotic bacteria are supplied with sulfide by Hb of the host animal and use it to provide carbon compounds. Here, we report the crystal structure of a 400-kDa Hb from pogonophoran Oligobrachia mashikoi at 2.85-A resolution. The structure is hollow-spherical, composed of a total of 24 globins as a dimer of dodecamer. This dodecameric assemblage would be a fundamental structural unit of both 400-kDa and 3,500-kDa Hbs. The structure of the mercury derivative used for phasing provides insights into the sulfide-binding mechanism. The mercury compounds bound to all free Cys residues that have been expected as sulfide-binding sites. Some of the free Cys residues are surrounded by Phe aromatic rings, and mercury atoms come into contact with these residues in the derivative structure. It is strongly suggested that sulfur atoms bound to these sites could be stabilized by aromatic-electrostatic interactions by the surrounding Phe residues.


    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic analysis of extracellular giant hemoglobin from pogonophoran Oligobrachia mashikoi.
      Numoto, N.,Nakagawa, T.,Kita, A.,Sasayama, Y.,Fukumori, Y.,Miki, K.
      (2005) Biochim.Biophys.Acta 1750: 173


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Giant hemoglobin, A1(b) globin chain
A
140Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbA1
Find proteins for Q7M419 (Oligobrachia mashikoi)
Go to UniProtKB:  Q7M419
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Giant hemoglobin, A2(a5) globin chain
B
142Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbA2
Find proteins for Q7M413 (Oligobrachia mashikoi)
Go to UniProtKB:  Q7M413
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Giant hemoglobin, B2(c) globin chain
C
147Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbB2
Find proteins for Q7M418 (Oligobrachia mashikoi)
Go to UniProtKB:  Q7M418
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Giant hemoglobin, B1(d) globin chain
D
145Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbB1
Find proteins for Q5KSB7 (Oligobrachia mashikoi)
Go to UniProtKB:  Q5KSB7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B, C, D
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 111.498α = 90.00
b = 111.498β = 90.00
c = 276.835γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
SOLVEphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance