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- PDB-5jdo: T. congolense haptoglobin-haemoglobin receptor in complex with ha... -

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Basic information

Entry
Database: PDB / ID: 5jdo
TitleT. congolense haptoglobin-haemoglobin receptor in complex with haemoglobin
Components
  • (Haptoglobin-haemoglobin ...) x 2
  • (Hemoglobin subunit ...) x 4
KeywordsOXYGEN TRANSPORT / Trypanosome / haptoglobin-haemoglobin receptor / haemoglobin / epimastigote
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
: / Haptoglobin-hemoglobin receptor / Ferritin - #80 / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Ferritin / Globin/Protoglobin / Globins ...: / Haptoglobin-hemoglobin receptor / Ferritin - #80 / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Ferritin / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Uncharacterized protein / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesTrypanosoma congolense (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLane-Serff, H. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)ML/L008246 United Kingdom
CitationJournal: Elife / Year: 2016
Title: Evolutionary diversification of the trypanosome haptoglobin-haemoglobin receptor from an ancestral haemoglobin receptor.
Authors: Lane-Serff, H. / MacGregor, P. / Peacock, L. / Macleod, O.J. / Kay, C. / Gibson, W. / Higgins, M.K. / Carrington, M.
History
DepositionApr 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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
Revision 1.4Nov 6, 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: Haptoglobin-haemoglobin receptor
B: Haptoglobin-haemoglobin receptor
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,86214
Polymers114,2686
Non-polymers2,5948
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16600 Å2
ΔGint-135 kcal/mol
Surface area46740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.750, 127.300, 172.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Haptoglobin-haemoglobin ... , 2 types, 2 molecules AB

#1: Protein Haptoglobin-haemoglobin receptor


Mass: 26563.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Gene: TCIL3000_10_2930 / Production host: Escherichia coli (E. coli) / References: UniProt: G0UVW6
#2: Protein Haptoglobin-haemoglobin receptor


Mass: 26117.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Gene: TCIL3000_10_2930 / Production host: Escherichia coli (E. coli) / References: UniProt: G0UVW6

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Hemoglobin subunit ... , 4 types, 4 molecules CDEF

#3: 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
#4: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15791.067 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
#5: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 14993.159 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
#6: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15652.920 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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Non-polymers , 2 types, 8 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 5, 8% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→102.41 Å / Num. obs: 26536 / % possible obs: 99 % / Redundancy: 2.7 % / Biso Wilson estimate: 93.75 Å2 / Rpim(I) all: 0.073 / Net I/σ(I): 7.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E40 and 1HH0

4e40

1hh0


Resolution: 3.2→102.41 Å / Cor.coef. Fo:Fc: 0.9152 / Cor.coef. Fo:Fc free: 0.9127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.412
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 1346 5.07 %RANDOM
Rwork0.2044 ---
obs0.206 26536 97.68 %-
Displacement parametersBiso mean: 87.29 Å2
Baniso -1Baniso -2Baniso -3
1--37.7025 Å20 Å20 Å2
2--14.4642 Å20 Å2
3---23.2383 Å2
Refine analyzeLuzzati coordinate error obs: 0.706 Å
Refinement stepCycle: 1 / Resolution: 3.2→102.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8046 0 180 0 8226
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018387HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2111411HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2935SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes210HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1218HARMONIC5
X-RAY DIFFRACTIONt_it8387HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion22.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1091SEMIHARMONIC5
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_contact9376SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.33 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3398 159 5.61 %
Rwork0.2716 2675 -
all0.2754 2834 -
obs--97.68 %
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)
10.0972-0.59380.40390.62990.23450-0.019-0.01840.044-0.11180.03140.0527-0.05590.0796-0.0124-0.18560.0188-0.0187-0.12480.0157-0.063621.7512178.74925.8364
20.02590.6904-0.46511.7589-1.28640.72280.02530.0196-0.0069-0.02520.0505-0.01950.04470.0871-0.0758-0.05820.1124-0.1023-0.22780.0955-0.1269.8834156.361-34.9667
30-0.4894-0.13140.60730.88930.20010.01290.1179-0.0743-0.0232-0.03660.05110.0699-0.00720.0237-0.0810.0296-0.0108-0.09460.022-0.03776.0942149.056-4.4271
40.4343-0.70351.24660.37352.35620.3867-0.0282-0.0890.08430.0450.0463-0.0133-0.12640.0448-0.0181-0.00310.05320.0293-0.09420.007-0.08584.3135170.4317.4038
50-0.22-0.431100.79410.59020.0006-0.11910.03990.08150.0259-0.0241-0.02150.0759-0.0265-0.06260.0620.00150.0199-0.0701-0.066235.2983161.1122.3374
60.0711-0.11750.687800.62550.27730.01110.07960.0093-0.1192-0.03410.0947-0.0639-0.00220.02310.007-0.02130.0797-0.0680.0599-0.135526.3502170.607-18.3351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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