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 

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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: https://doi.org/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 (Hb) complexes ...

    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
A, F, K, P, U, Z
A, F, K, P, U, Z
141Homo sapiensMutation(s): 0 
Gene Names: HBA1, HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
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PHAROS:  P69905
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UniProt GroupP69905
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit beta146Homo sapiensMutation(s): 0 
Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
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PHAROS:  P68871
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UniProt GroupP68871
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Haptoglobin315Homo sapiensMutation(s): 0 
Gene Names: HP
UniProt & NIH Common Fund Data Resources
Find proteins for P00738 (Homo sapiens)
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PHAROS:  P00738
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UniProt GroupP00738
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-regulated surface determinant protein H146Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: isdH, harA, sasI, SA1552
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Find proteins for Q99TD3 (Staphylococcus aureus (strain N315))
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UniProt GroupQ99TD3
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Haptoglobin-hemoglobin receptor343Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: HpHbR
UniProt
Find proteins for I7BA80 (Trypanosoma brucei brucei)
Explore I7BA80 
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UniProt GroupI7BA80
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Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
EA [auth a],
FA [auth b],
GA [auth c],
HA [auth d],
IA [auth e],
EA [auth a],
FA [auth b],
GA [auth c],
HA [auth d],
IA [auth e],
JA [auth f],
KA [auth g],
LA [auth h],
MA [auth i],
NA [auth j]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
CC [auth Z],
EB [auth K],
EC [auth 1],
GB [auth L],
MB [auth P],
CC [auth Z],
EB [auth K],
EC [auth 1],
GB [auth L],
MB [auth P],
OA [auth A],
OB [auth Q],
QA [auth B],
UB [auth U],
WA [auth F],
WB [auth V],
YA [auth G]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
NAG
Query on NAG
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AB [auth H],
AC [auth Y],
BB [auth H],
BC [auth Y],
CB [auth J],
AB [auth H],
AC [auth Y],
BB [auth H],
BC [auth Y],
CB [auth J],
DB [auth J],
GC [auth 2],
HC [auth 4],
IB [auth M],
IC [auth 4],
JB [auth M],
KB [auth O],
LB [auth O],
QB [auth R],
RB [auth R],
SA [auth C],
SB [auth T],
TA [auth C],
TB [auth T],
UA [auth E],
VA [auth E],
YB [auth W],
ZB [auth W]
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 
DC [auth Z],
FB [auth K],
FC [auth 1],
HB [auth L],
NB [auth P],
DC [auth Z],
FB [auth K],
FC [auth 1],
HB [auth L],
NB [auth P],
PA [auth A],
PB [auth Q],
RA [auth B],
VB [auth U],
XA [auth F],
XB [auth V],
ZA [auth G]
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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Ligand Structure Quality Assessment 


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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  (Full details and data files)

  • 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