3WCT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 2.0 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 D Biol Crystallogr 70: 1823-1831

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

  • 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 ...

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
A1 globin chain of giant V2 hemoglobinA, E146Lamellibrachia satsumaMutation(s): 0 
Gene Names: v2hb-A1
Find proteins for S0BBU7 (Lamellibrachia satsuma)
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Go to UniProtKB:  S0BBU7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
A2 globin chain of giant V2 hemoglobinB, F144Lamellibrachia satsumaMutation(s): 0 
Gene Names: v2hb-A2ghbA2
Find proteins for S0BBR6 (Lamellibrachia satsuma)
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Go to UniProtKB:  S0BBR6
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
B2 globin chain of giant V2 hemoglobinC, G150Lamellibrachia satsumaMutation(s): 0 
Gene Names: v2hb-B2ghbB2
Find proteins for S0BCU7 (Lamellibrachia satsuma)
Explore S0BCU7 
Go to UniProtKB:  S0BCU7
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
B1 globin chain of giant V2 hemoglobinD, H149Lamellibrachia satsumaMutation(s): 0 
Gene Names: v2hb-B1
Find proteins for S0BAP9 (Lamellibrachia satsuma)
Explore S0BAP9 
Go to UniProtKB:  S0BAP9
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseI, J6 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth H], K [auth A], M [auth B], P [auth C], R [auth D], T [auth E], V [auth F], Y [auth G]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
O [auth B], X [auth F]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
OXY
Query on OXY

Download Ideal Coordinates CCD File 
BA [auth H], L [auth A], N [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Z [auth G]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.556α = 90
b = 108.556β = 90
c = 193.552γ = 120
Software Package:
Software NamePurpose
BSSdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-08-06
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary