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- PDB-5hu6: Structure of the T. brucei haptoglobin-haemoglobin receptor bound... -

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Basic information

Entry
Database: PDB / ID: 5hu6
TitleStructure of the T. brucei haptoglobin-haemoglobin receptor bound to human haptolgobin-haemoglobin
Components
  • (Hemoglobin subunit ...) x 2
  • Haptoglobin
  • Haptoglobin-hemoglobin receptor
KeywordsTRANSPORT PROTEIN / Trypanosome haptoglobin-haemoglobin
Function / homology
Function and homology information


ciliary pocket / negative regulation of hydrogen peroxide catabolic process / heme transmembrane transporter activity / zymogen activation / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption ...ciliary pocket / negative regulation of hydrogen peroxide catabolic process / heme transmembrane transporter activity / zymogen activation / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / antioxidant activity / hemoglobin complex / oxygen transport / immune system process / Scavenging of heme from plasma / endocytic vesicle lumen / receptor-mediated endocytosis / blood vessel diameter maintenance / acute-phase response / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Heme signaling / defense response / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / platelet aggregation / regulation of blood pressure / specific granule lumen / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / response to oxidative stress / blood microparticle / ficolin-1-rich granule lumen / defense response to bacterium / iron ion binding / inflammatory response / serine-type endopeptidase activity / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
: / Haptoglobin-hemoglobin receptor / Ferritin - #80 / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : ...: / Haptoglobin-hemoglobin receptor / Ferritin - #80 / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Ferritin / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Haptoglobin-hemoglobin receptor / Haptoglobin / Hemoglobin subunit beta / Hemoglobin subunit alpha / Haptoglobin-hemoglobin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Trypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLane-Serff, H. / Higgins, M.K.
CitationJournal: Elife / Year: 2014
Title: Structural basis for ligand and innate immunity factor uptake by the trypanosome haptoglobin-haemoglobin receptor.
Authors: Lane-Serff, H. / MacGregor, P. / Lowe, E.D. / Carrington, M. / Higgins, M.K.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionMar 2, 2016ID: 4X0I
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Haptoglobin
D: Haptoglobin-hemoglobin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,83310
Polymers87,0944
Non-polymers1,7396
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-59 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.290, 56.560, 66.100
Angle α, β, γ (deg.)90.00, 92.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Hemoglobin subunit ... , 2 types, 2 molecules AB

#1: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15222.419 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Homo sapiens (human) / References: UniProt: P68871

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Protein , 2 types, 2 molecules CD

#3: Protein Haptoglobin / Zonulin


Mass: 28790.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00738
#4: Protein Haptoglobin-hemoglobin receptor


Mass: 27930.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HpHbR / Production host: Escherichia coli (E. coli) / References: UniProt: I7B1A7, UniProt: Q581F2*PLUS

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Sugars , 1 types, 2 molecules

#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5% v/v MPD, 0.03 M NaBr, 0.03M NaI, 0.03M NaF, 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.9→66 Å / Num. obs: 18486 / % possible obs: 99.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 76.4 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOL

4xol


Resolution: 2.9→58.07 Å / Cor.coef. Fo:Fc: 0.9219 / Cor.coef. Fo:Fc free: 0.8765 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.368
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 923 5.06 %RANDOM
Rwork0.1902 ---
obs0.192 18253 98.68 %-
Displacement parametersBiso mean: 67.95 Å2
Baniso -1Baniso -2Baniso -3
1--12.6868 Å20 Å2-5.0989 Å2
2--18.1527 Å20 Å2
3----5.4659 Å2
Refine analyzeLuzzati coordinate error obs: 0.441 Å
Refinement stepCycle: 1 / Resolution: 2.9→58.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5998 0 118 0 6116
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016248HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.178494HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2166SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes906HARMONIC5
X-RAY DIFFRACTIONt_it6248HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion20.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion814SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7142SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2483 119 4.12 %
Rwork0.2351 2772 -
all0.2357 2891 -
obs--98.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.519-0.0473-1.32142.1363-0.31334.3148-0.0337-0.33560.2747-0.004-0.0014-0.7398-0.45410.76680.0351-0.194-0.1643-0.1175-0.001-0.1283-0.003253.125536.039512.3792
25.1621.1825-3.03461.2914-1.00924.2697-0.4235-0.5726-0.96510.25470.0185-0.32080.64910.87910.405-0.05160.2413-0.0797-0.15960.09960.067242.50617.193723.2236
32.60260.46160.50222.22210.26113.7942-0.33810.42060.0516-0.20610.40210.1679-0.3995-0.1481-0.064-0.0995-0.075-0.0992-0.17720.0458-0.064925.388334.768-2.3998
40.7933-2.04490.12714.97480.5090.4044-0.0906-0.1318-0.22160.29180.14240.41080.1429-0.1665-0.0519-0.10630.16030.107-0.19740.16170.114210.66331.690124.7413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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