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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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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 (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 alphaA, F, K, P, U, Z141Homo sapiensMutation(s): 0 
Gene Names: HBA1HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
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PHAROS:  P69905
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit betaAA [auth 1], B, G, L, Q, V146Homo 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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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HaptoglobinBA [auth 2], C, H, M, R, W315Homo 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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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-regulated surface determinant protein HCA [auth 3], D, I, N, S, X146Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: isdHharAsasISA1552
UniProt
Find proteins for Q99TD3 (Staphylococcus aureus (strain N315))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Haptoglobin-hemoglobin receptorDA [auth 4], E, J, O, T, Y343Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: HpHbR
UniProt
Find proteins for I7BA80 (Trypanosoma brucei brucei)
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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], JA [auth f], KA [auth g], LA [auth h]
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 (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
CC [auth Z] , EB [auth K] , EC [auth 1] , GB [auth L] , MB [auth P] , OA [auth A] , OB [auth Q] , QA [auth B] , 
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 (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth H] , AC [auth Y] , BB [auth H] , BC [auth Y] , CB [auth J] , DB [auth J] , GC [auth 2] , HC [auth 4] , 
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] , PA [auth A] , PB [auth Q] , RA [auth B] , 
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  



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