Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Hetero 24-mer - A6B6C6D6 Pseudo Symmetry: Dihedral - D3  (3D View)
Pseudo Stoichiometry: Homo 24-mer -A24 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 137443.70 
• Atom Count: 9626 
• Residue Count: 1178 
• Unique protein chains: 4

3WCU

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

• DOI: 10.2210/pdb3WCU/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Lamellibrachia satsuma


• Deposited: 2013-06-01 Released: 2014-06-04 
• Deposition Author(s): Numoto, N., Nakagawa, T., Ohara, R., Hasegawa, T., Kita, A., Yoshida, T., Maruyama, T., Imai, K., Fukumori, Y., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.292 
• R-Value Work: 0.246 

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

• PubMed: 25004960 
• DOI: 10.1107/S1399004714008475
• Primary Citation of Related Structures:  
  3WCW, 3WCV, 3WCT


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
A1 globin chain of giant V2 hemoglobin	A, E	146	Lamellibrachia satsuma	Mutation(s): 0  Gene Names: v2hb-A1
Find proteins for S0BBU7 (Lamellibrachia satsuma) Go to UniProtKB:  S0BBU7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
A2 globin chain of giant V2 hemoglobin	B, F	144	Lamellibrachia satsuma	Mutation(s): 0  Gene Names: v2hb-A2 (ghbA2)
Find proteins for S0BBR6 (Lamellibrachia satsuma) Go to UniProtKB:  S0BBR6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
B2 globin chain of giant V2 hemoglobin	C, G	150	Lamellibrachia satsuma	Mutation(s): 0  Gene Names: v2hb-B2 (ghbB2)
Find proteins for S0BCU7 (Lamellibrachia satsuma) Go to UniProtKB:  S0BCU7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
B1 globin chain of giant V2 hemoglobin	D, H	149	Lamellibrachia satsuma	Mutation(s): 0  Gene Names: v2hb-B1
Find proteins for S0BAP9 (Lamellibrachia satsuma) Go to UniProtKB:  S0BAP9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	B, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	D, H	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	D, H	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
HEM	A, B, C, D, E, F, G, H	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG	D, H	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.292 
• R-Value Work: 0.246 
• Space Group: P 6₃

Unit Cell:

Length (Å)	Angle (°)
a = 108.872	α = 90.00
b = 108.872	β = 90.00
c = 195.157	γ = 120.00

Software Package:

Software Name	Purpose
BSS	data collection
CNS	phasing
HKL-2000	data reduction
CNS	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-01 
• Released Date: 2014-06-04 
• Deposition Author(s): Numoto, N., Nakagawa, T., Ohara, R., Hasegawa, T., Kita, A., Yoshida, T., Maruyama, T., Imai, K., Fukumori, Y., Miki, K.

Revision History 

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