5X2S

Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 4 mM bezafibrate pH 6.5.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Direct observation of conformational population shifts in crystalline human hemoglobin.

Shibayama, N.Ohki, M.Tame, J.R.H.Park, S.Y.

(2017) J. Biol. Chem. 292: 18258-18269

  • DOI: 10.1074/jbc.M117.781146
  • Primary Citation of Related Structures:  5X2R, 5X2T, 5X2U

  • PubMed Abstract: 
  • Although X-ray crystallography is the most commonly used technique for studying the molecular structure of proteins, it is not generally able to monitor the dynamic changes or global domain motions that often underlie allostery. These motions often p ...

    Although X-ray crystallography is the most commonly used technique for studying the molecular structure of proteins, it is not generally able to monitor the dynamic changes or global domain motions that often underlie allostery. These motions often prevent crystal growth or reduce crystal order. We have recently discovered a crystal form of human hemoglobin that contains three protein molecules allowed to express a full range of quaternary structures, whereas maintaining strong X-ray diffraction. Here we use this crystal form to investigate the effects of two allosteric effectors, phosphate and bezafibrate, by tracking the structures and functions of the three hemoglobin molecules following the addition of each effector. The X-ray analysis shows that the addition of either phosphate or bezafibrate not only induces conformational changes in a direction from a relaxed-state to a tense-state, but also within relaxed-state populations. The microspectrophotometric O2 equilibrium measurements on the crystals demonstrate that the binding of each effector energetically stabilizes the lowest affinity conformer more strongly than the intermediate affinity one, thereby reducing the O2 affinity of tense-state populations, and that the addition of bezafibrate causes an ∼5-fold decrease in the O2 affinity of relaxed-state populations. These results show that the allosteric pathway of hemoglobin involves shifts of populations rather than a unidirectional conversion of one quaternary structure to another, and that minor conformers of hemoglobin may have a disproportionate effect on the overall O2 affinity.


    Organizational Affiliation

    From the Department of Physiology, Division of Biophysics, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 and shibayam@jichi.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A, C, E, G, I, K
141Homo sapiensGene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B, D, F, H, J, L
146Homo sapiensGene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEM
Query on PEM

Download SDF File 
Download CCD File 
I
2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID
C19 H20 Cl N O4
IIBYAHWJQTYFKB-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
B, C, F, G, J, K
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HNI
Query on HNI

Download SDF File 
Download CCD File 
A, D, E, H, I, L
PROTOPORPHYRIN IX CONTAINING NI(II)
C34 H32 N4 Ni O4
IJROJBFZULUEEG-QFCVZVLGDG
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 228.603α = 90.00
b = 54.598β = 103.18
c = 138.444γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
BUSTERrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-02-02 
  • Released Date: 2017-09-27 
  • Deposition Author(s): Ohki, M., Park, S.-Y.

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-12-20
    Type: Database references