3WCW

The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: MG bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins

Numoto, N.Nakagawa, T.Ohara, R.Hasegawa, T.Kita, A.Yoshida, T.Maruyama, T.Imai, K.Fukumori, Y.Miki, K.

(2014) Acta Crystallogr.,Sect.D 70: 1823-1831

  • DOI: 10.1107/S1399004714008475
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The quaternary structures of invertebrate haemoglobins (Hbs) are quite different from those of vertebrate Hbs. The extracellular giant Hbs of molecular masses of about 400 and 3600 kDa are composed of a dome-shaped dodecameric subassembly which consi ...

    The quaternary structures of invertebrate haemoglobins (Hbs) are quite different from those of vertebrate Hbs. The extracellular giant Hbs of molecular masses of about 400 and 3600 kDa are composed of a dome-shaped dodecameric subassembly which consists of four individual globin subunits. Several crystal structures of 400 kDa Hbs from annelids have been reported, including structures in oxygenated and partially unliganded states, but the structure of the fully deoxygenated state has not been reported. In the present study, crystal structures of V2Hb from the tube worm Lamellibrachia satsuma have been determined in both the fully oxygenated and deoxygenated states. A glycosylation site and novel metal-binding sites for divalent cations were clearly observed with no intersubunit interactions in V2Hb. A comparison of the oxygenated and the deoxygenated forms of V2Hb reveals that the ternary- and quaternary-structural changes occur in a manner that maintains the molecular D3 symmetry. These structures suggest that the mechanisms of quaternary-structural changes between the oxy and deoxy states for the giant Hbs are identical across species.


    Organizational Affiliation

    Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A1 globin chain of giant V2 hemoglobin
A, E
146Lamellibrachia satsumaMutation(s): 0 
Gene Names: v2hb-A1
Find proteins for S0BBU7 (Lamellibrachia satsuma)
Go to UniProtKB:  S0BBU7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
A2 globin chain of giant V2 hemoglobin
B, F
144Lamellibrachia satsumaMutation(s): 0 
Gene Names: v2hb-A2 (ghbA2)
Find proteins for S0BBR6 (Lamellibrachia satsuma)
Go to UniProtKB:  S0BBR6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
B2 globin chain of giant V2 hemoglobin
C, G
150Lamellibrachia satsumaMutation(s): 0 
Gene Names: v2hb-B2 (ghbB2)
Find proteins for S0BCU7 (Lamellibrachia satsuma)
Go to UniProtKB:  S0BCU7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
B1 globin chain of giant V2 hemoglobin
D, H
149Lamellibrachia satsumaMutation(s): 0 
Gene Names: v2hb-B1
Find proteins for S0BAP9 (Lamellibrachia satsuma)
Go to UniProtKB:  S0BAP9
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
D, H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
D, H
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B, C, D, E, F, G, H
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
D, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 109.273α = 90.00
b = 109.273β = 90.00
c = 195.599γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
CNSphasing
BSSdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-08-06
    Type: Database references