4WJG

Structure of T. brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report



Literature

Structural basis for trypanosomal haem acquisition and susceptibility to the host innate immune system.

Stdkilde, K.Torvund-Jensen, M.Moestrup, S.K.Andersen, C.B.

(2014) Nat Commun 5: 5487-5487

  • DOI: 10.1038/ncomms6487
  • Primary Citation of Related Structures:  
    4WJG

  • PubMed Abstract: 
  • Sleeping sickness is caused by trypanosome parasites, which infect humans and livestock in Sub-Saharan Africa. Haem is an important growth factor for the parasites and is acquired from the host by receptor-mediated uptake of haptoglobin (Hp)-haemoglobin ...

    Sleeping sickness is caused by trypanosome parasites, which infect humans and livestock in Sub-Saharan Africa. Haem is an important growth factor for the parasites and is acquired from the host by receptor-mediated uptake of haptoglobin (Hp)-haemoglobin (Hb) complexes. The parasite Hp-Hb receptor (HpHbR) is also a target for a specialized innate immune defence executed by trypanosome-killing lipoprotein particles containing an Hp-related protein in complex with Hb. Here we report the structure of the multimeric complex between human Hp-Hb and Trypanosoma brucei brucei HpHbR. Two receptors forming kinked three-helical rods with small head regions bind to Hp and the β-subunits of Hb (βHb), with one receptor at each end of the dimeric Hp-Hb complex. The Hb β-subunit haem group directly associates with the receptors, which allows for sensing of haem-containing Hp-Hb. The HpHbR-binding region of Hp is conserved in Hp-related protein, indicating an identical recognition of Hp-Hb and trypanolytic particles by HpHbR in human plasma.


    Organizational Affiliation

    Department of Biomedicine, Aarhus University, Ole Worms Allé 3, DK-8000 Aarhus C, Denmark.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit alpha AFKPUZ141Homo sapiensMutation(s): 0 
Gene Names: HBA1HBA2
Find proteins for P69905 (Homo sapiens)
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PHAROS:  P69905
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit beta 1BGLQV146Homo sapiensMutation(s): 0 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
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PHAROS:  P68871
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Haptoglobin 2CHMRW315Homo sapiensMutation(s): 0 
Gene Names: HP
Find proteins for P00738 (Homo sapiens)
Explore P00738 
Go to UniProtKB:  P00738
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PHAROS:  P00738
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-regulated surface determinant protein H 3DINSX146Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: isdHharAsasISA1552
Find proteins for Q99TD3 (Staphylococcus aureus (strain N315))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Haptoglobin-hemoglobin receptor 4EJOTY343Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: HpHbR
Find proteins for I7BA80 (Trypanosoma brucei brucei)
Explore I7BA80 
Go to UniProtKB:  I7BA80
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
a, b, c, d, e, f, g, h, i, j
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
1, A, B, F, G, K, L, P, Q, U, V, Z
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
2, 4, C, E, H, J, M, O, R, T, W, Y
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
OXY
Query on OXY

Download Ideal Coordinates CCD File 
1, A, B, F, G, K, L, P, Q, U, V, Z
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.23α = 90
b = 140.95β = 98.54
c = 267.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Lundbeck FoundationDenmark--
The Novo Nordisk FoundationDenmark--
The European Research CouncilDenmark--
The Danish Council for Independent ResearchDenmark--

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2018-02-28
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary