4WJG

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

PDB DOI: https://doi.org/10.2210/pdb4WJG/pdb

Classification: ENDOCYTOSIS
Organism(s): Homo sapiens, Staphylococcus aureus subsp. aureus N315, Trypanosoma brucei brucei
Expression System: Escherichia coli BL21(DE3), Komagataella pastoris
Mutation(s): No

Deposited: 2014-09-30 Released: 2014-11-26
Deposition Author(s): Stoedkilde, K., Torvund-Jensen, M., Moestrup, S.K., Andersen, C.B.F.
Funding Organization(s): The Lundbeck Foundation, The Novo Nordisk Foundation, The European Research Council, The Danish Council for Independent Research

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

Ligand Structure Quality Assessment

This is version 2.1 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

PubMed: 25410714 Search on PubMed
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. 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.

Macromolecule Content

Total Structure Weight: 737.32 kDa
Atom Count: 47,792
Modelled Residue Count: 6,012
Deposited Residue Count: 6,546
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, F, K, P, U A, F, K, P, U, Z	141	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905 Go to UniProtKB: P69905
PHAROS: P69905 GTEx: ENSG00000188536 ENSG00000206172
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69905
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	AA [auth 1] B G L Q AA [auth 1], B, G, L, Q, V	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871 Go to UniProtKB: P68871
PHAROS: P68871 GTEx: ENSG00000244734
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68871
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Haptoglobin	BA [auth 2] C H M R BA [auth 2], C, H, M, R, W	315	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P00738 (Homo sapiens) Explore P00738 Go to UniProtKB: P00738
PHAROS: P00738 GTEx: ENSG00000257017
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00738
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain BA [auth 2] Focus chain C Focus chain H Focus chain M Focus chain R Focus chain W	Go to GlyGen: P00738-1
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-regulated surface determinant protein H	CA [auth 3] D I N S CA [auth 3], D, I, N, S, X	146	Staphylococcus aureus subsp. aureus N315	Mutation(s): 0 Gene Names: isdH, harA, sasI, SA1552
UniProt
Find proteins for Q99TD3 (Staphylococcus aureus (strain N315)) Explore Q99TD3 Go to UniProtKB: Q99TD3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99TD3
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Haptoglobin-hemoglobin receptor	DA [auth 4] E J O T DA [auth 4], E, J, O, T, Y	343	Trypanosoma brucei brucei	Mutation(s): 0 Gene Names: HpHbR
UniProt
Find proteins for I7BA80 (Trypanosoma brucei brucei) Explore I7BA80 Go to UniProtKB: I7BA80
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7BA80
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain DA [auth 4] Focus chain E Focus chain J Focus chain O Focus chain T Focus chain Y
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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]	2		N-Glycosylation	Interactions Focus chain EA [auth a] Focus chain FA [auth b] Focus chain GA [auth c] Focus chain HA [auth d] Focus chain IA [auth e] Focus chain JA [auth f] Focus chain KA [auth g] Focus chain LA [auth h] Focus chain MA [auth i] Focus chain NA [auth j] Interactions & Density Focus chain EA [auth a] Focus chain FA [auth b] Focus chain GA [auth c] Focus chain HA [auth d] Focus chain IA [auth e] Focus chain JA [auth f] Focus chain KA [auth g] Focus chain LA [auth h] Focus chain MA [auth i] Focus chain NA [auth j]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain CC [auth Z] SDF format, chain EB [auth K] SDF format, chain EC [auth 1] SDF format, chain GB [auth L] SDF format, chain MB [auth P] SDF format, chain OA [auth A] SDF format, chain OB [auth Q] SDF format, chain QA [auth B] SDF format, chain UB [auth U] SDF format, chain WA [auth F] SDF format, chain WB [auth V] SDF format, chain YA [auth G] MOL2 format, chain CC [auth Z] MOL2 format, chain EB [auth K] MOL2 format, chain EC [auth 1] MOL2 format, chain GB [auth L] MOL2 format, chain MB [auth P] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth Q] MOL2 format, chain QA [auth B] MOL2 format, chain UB [auth U] MOL2 format, chain WA [auth F] MOL2 format, chain WB [auth V] MOL2 format, chain YA [auth G] mmCIF format, chain CC [auth Z] mmCIF format, chain EB [auth K] mmCIF format, chain EC [auth 1] mmCIF format, chain GB [auth L] mmCIF format, chain MB [auth P] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth Q] mmCIF format, chain QA [auth B] mmCIF format, chain UB [auth U] mmCIF format, chain WA [auth F] mmCIF format, chain WB [auth V] mmCIF format, chain YA [auth G]	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		Interactions Focus chain CC [auth Z] Focus chain EB [auth K] Focus chain EC [auth 1] Focus chain GB [auth L] Focus chain MB [auth P] Focus chain OA [auth A] Focus chain OB [auth Q] Focus chain QA [auth B] Focus chain UB [auth U] Focus chain WA [auth F] Focus chain WB [auth V] Focus chain YA [auth G] Interactions & Density Focus chain CC [auth Z] Focus chain EB [auth K] Focus chain EC [auth 1] Focus chain GB [auth L] Focus chain MB [auth P] Focus chain OA [auth A] Focus chain OB [auth Q] Focus chain QA [auth B] Focus chain UB [auth U] Focus chain WA [auth F] Focus chain WB [auth V] Focus chain YA [auth G]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain AC [auth Y] SDF format, chain BB [auth H] SDF format, chain BC [auth Y] SDF format, chain CB [auth J] SDF format, chain DB [auth J] SDF format, chain GC [auth 2] SDF format, chain HC [auth 4] SDF format, chain IB [auth M] SDF format, chain IC [auth 4] SDF format, chain JB [auth M] SDF format, chain KB [auth O] SDF format, chain LB [auth O] SDF format, chain QB [auth R] SDF format, chain RB [auth R] SDF format, chain SA [auth C] SDF format, chain SB [auth T] SDF format, chain TA [auth C] SDF format, chain TB [auth T] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain YB [auth W] SDF format, chain ZB [auth W] MOL2 format, chain AB [auth H] MOL2 format, chain AC [auth Y] MOL2 format, chain BB [auth H] MOL2 format, chain BC [auth Y] MOL2 format, chain CB [auth J] MOL2 format, chain DB [auth J] MOL2 format, chain GC [auth 2] MOL2 format, chain HC [auth 4] MOL2 format, chain IB [auth M] MOL2 format, chain IC [auth 4] MOL2 format, chain JB [auth M] MOL2 format, chain KB [auth O] MOL2 format, chain LB [auth O] MOL2 format, chain QB [auth R] MOL2 format, chain RB [auth R] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth T] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth T] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain YB [auth W] MOL2 format, chain ZB [auth W] mmCIF format, chain AB [auth H] mmCIF format, chain AC [auth Y] mmCIF format, chain BB [auth H] mmCIF format, chain BC [auth Y] mmCIF format, chain CB [auth J] mmCIF format, chain DB [auth J] mmCIF format, chain GC [auth 2] mmCIF format, chain HC [auth 4] mmCIF format, chain IB [auth M] mmCIF format, chain IC [auth 4] mmCIF format, chain JB [auth M] mmCIF format, chain KB [auth O] mmCIF format, chain LB [auth O] mmCIF format, chain QB [auth R] mmCIF format, chain RB [auth R] mmCIF format, chain SA [auth C] mmCIF format, chain SB [auth T] mmCIF format, chain TA [auth C] mmCIF format, chain TB [auth T] mmCIF format, chain UA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain YB [auth W] mmCIF format, chain ZB [auth W]	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		Interactions Focus chain AB [auth H] Focus chain AC [auth Y] Focus chain BB [auth H] Focus chain BC [auth Y] Focus chain CB [auth J] Focus chain DB [auth J] Focus chain GC [auth 2] Focus chain HC [auth 4] Focus chain IB [auth M] Focus chain IC [auth 4] Focus chain JB [auth M] Focus chain KB [auth O] Focus chain LB [auth O] Focus chain QB [auth R] Focus chain RB [auth R] Focus chain SA [auth C] Focus chain SB [auth T] Focus chain TA [auth C] Focus chain TB [auth T] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain YB [auth W] Focus chain ZB [auth W] Interactions & Density Focus chain AB [auth H] Focus chain AC [auth Y] Focus chain BB [auth H] Focus chain BC [auth Y] Focus chain CB [auth J] Focus chain DB [auth J] Focus chain GC [auth 2] Focus chain HC [auth 4] Focus chain IB [auth M] Focus chain IC [auth 4] Focus chain JB [auth M] Focus chain KB [auth O] Focus chain LB [auth O] Focus chain QB [auth R] Focus chain RB [auth R] Focus chain SA [auth C] Focus chain SB [auth T] Focus chain TA [auth C] Focus chain TB [auth T] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain YB [auth W] Focus chain ZB [auth W]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain DC [auth Z] SDF format, chain FB [auth K] SDF format, chain FC [auth 1] SDF format, chain HB [auth L] SDF format, chain NB [auth P] SDF format, chain PA [auth A] SDF format, chain PB [auth Q] SDF format, chain RA [auth B] SDF format, chain VB [auth U] SDF format, chain XA [auth F] SDF format, chain XB [auth V] SDF format, chain ZA [auth G] MOL2 format, chain DC [auth Z] MOL2 format, chain FB [auth K] MOL2 format, chain FC [auth 1] MOL2 format, chain HB [auth L] MOL2 format, chain NB [auth P] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth Q] MOL2 format, chain RA [auth B] MOL2 format, chain VB [auth U] MOL2 format, chain XA [auth F] MOL2 format, chain XB [auth V] MOL2 format, chain ZA [auth G] mmCIF format, chain DC [auth Z] mmCIF format, chain FB [auth K] mmCIF format, chain FC [auth 1] mmCIF format, chain HB [auth L] mmCIF format, chain NB [auth P] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth Q] mmCIF format, chain RA [auth B] mmCIF format, chain VB [auth U] mmCIF format, chain XA [auth F] mmCIF format, chain XB [auth V] mmCIF format, chain ZA [auth G]	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		Interactions Focus chain DC [auth Z] Focus chain FB [auth K] Focus chain FC [auth 1] Focus chain HB [auth L] Focus chain NB [auth P] Focus chain PA [auth A] Focus chain PB [auth Q] Focus chain RA [auth B] Focus chain VB [auth U] Focus chain XA [auth F] Focus chain XB [auth V] Focus chain ZA [auth G] Interactions & Density Focus chain DC [auth Z] Focus chain FB [auth K] Focus chain FC [auth 1] Focus chain HB [auth L] Focus chain NB [auth P] Focus chain PA [auth A] Focus chain PB [auth Q] Focus chain RA [auth B] Focus chain VB [auth U] Focus chain XA [auth F] Focus chain XB [auth V] Focus chain ZA [auth G]

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 = 143.23	α = 90
b = 140.95	β = 98.54
c = 267.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Funding Organization	Location	Grant Number
The Lundbeck Foundation	Denmark	--
The Novo Nordisk Foundation	Denmark	--
The European Research Council	Denmark	--
The Danish Council for Independent Research	Denmark	--

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
Version 2.1: 2024-10-16
Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Help and Resources

4WJG

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt

Entity Groups

Glycosylation

Sequence Annotations

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Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)