Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer -A4 

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

Macromolecule Content

• Total Structure Weight: 64643.11 
• Atom Count: 4557 
• Residue Count: 574 
• Unique protein chains: 2

1DKE

NI BETA HEME HUMAN HEMOGLOBIN

• DOI: 10.2210/pdb1DKE/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Homo sapiens


• Deposited: 1999-12-07 Released: 2000-05-23 
• Deposition Author(s): Bruno, S., Bettatti, S., Mozzarelli, A., Bolognesi, M., Deriu, D., Rosano, C., Tsuneshige, A., Yonetani, T., Henry, E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.280 
• R-Value Work: 0.200 

Literature

Oxygen binding by alpha(Fe2+)2beta(Ni2+)2 hemoglobin crystals.

Bruno, S., Bettati, S., Manfredini, M., Mozzarelli, A., Bolognesi, M., Deriu, D., Rosano, C., Tsuneshige, A., Yonetani, T., Henry, E.R.

(2000) Protein Sci. 9: 683-692

• PubMed: 10794410 
• DOI: 10.1110/ps.9.4.683


• PubMed Abstract: 
  

Oxygen binding by hemoglobin fixed in the T state either by crystallization or by encapsulation in silica gels is apparently noncooperative. However, cooperativity might be masked by different oxygen affinities of alpha and beta subunits. Metal hybrid hemoglobins, where the noniron metal does not bind oxygen, provide the opportunity to determine the oxygen affinities of alpha and beta hemes separately. Previous studies have characterized the oxygen binding by alpha(Ni2+)2beta(Fe2+)2 crystals. Here, we have determined the three-dimensional (3D) structure and oxygen binding of alpha(Fe2+)2beta(Ni2+)2 crystals grown from polyethylene glycol solutions. Polarized absorption spectra were recorded at different oxygen pressures with light polarized parallel either to the b or c crystal axis by single crystal microspectrophotometry. The oxygen pressures at 50% saturation (p50s) are 95 +/- 3 and 87 +/- 4 Torr along the b and c crystal axes, respectively, and the corresponding Hill coefficients are 0.96 +/- 0.06 and 0.90 +/- 0.03. Analysis of the binding curves, taking into account the different projections of the alpha hemes along the optical directions, indicates that the oxygen affinity of alpha1 hemes is 1.3-fold lower than alpha2 hemes. Inspection of the 3D structure suggests that this inequivalence may arise from packing interactions of the Hb tetramer within the monoclinic crystal lattice. A similar inequivalence was found for the beta subunits of alpha(Ni2+)2beta(Fe2+)2 crystals. The average oxygen affinity of the alpha subunits (p50 = 91 Torr) is about 1.2-fold higher than the beta subunits (p50 = 110 Torr). In the absence of cooperativity, this heterogeneity yields an oxygen binding curve of Hb A with a Hill coefficient of 0.999. Since the binding curves of Hb A crystals exhibit a Hill coefficient very close to unity, these findings indicate that oxygen binding by T-state hemoglobin is noncooperative, in keeping with the Monod, Wyman, and Changeux model.

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Organizational Affiliation: 

Institute of Biochemical Sciences, University of Parma, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HEMOGLOBIN: ALPHA CHAIN	A, C	141	Homo sapiens	Mutation(s): 0  Gene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens) Go to Gene View: HBA1 HBA2 Go to UniProtKB:  P69905

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HEMOGLOBIN: BETA CHAIN	B, D	146	Homo sapiens	Mutation(s): 0  Gene Names: HBB
Find proteins for P68871 (Homo sapiens) Go to Gene View: HBB Go to UniProtKB:  P68871

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
HEM	A, B, C, D	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.280 
• R-Value Work: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 55.720	α = 90.00
b = 81.400	β = 97.81
c = 63.150	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
ROTAVATA	data scaling
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-12-07 
• Released Date: 2000-05-23 
• Deposition Author(s): Bruno, S., Bettatti, S., Mozzarelli, A., Bolognesi, M., Deriu, D., Rosano, C., Tsuneshige, A., Yonetani, T., Henry, E.R.

Revision History 

• Version 1.0: 2000-05-23
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-04
  Type: Advisory, Refinement description
• Version 1.4: 2018-01-31
  Type: Experimental preparation