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- PDB-6soy: Trypanosoma brucei transferrin receptor in complex with human tra... -

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Basic information

Entry
Database: PDB / ID: 6soy
TitleTrypanosoma brucei transferrin receptor in complex with human transferrin
Components
  • ESAG6, subunit of heterodimeric transferrin receptor
  • ESAG7, subunit of heterodimeric transferrin receptor
  • Serotransferrin
KeywordsPROTEIN BINDING / Trypanosoma brucei Trypanosome Transferrin receptor Transferrrin Cell surface
Function / homology
Function and homology information


ciliary pocket / transferrin receptor activity / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / evasion of host immune response / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption ...ciliary pocket / transferrin receptor activity / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / evasion of host immune response / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / positive regulation of phosphorylation / clathrin-coated pit / side of membrane / ERK1 and ERK2 cascade / osteoclast differentiation / ferric iron binding / basal plasma membrane / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / ferrous iron binding / regulation of iron ion transport / regulation of protein stability / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Cargo recognition for clathrin-mediated endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / antibacterial humoral response / Clathrin-mediated endocytosis / iron ion transport / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / blood microparticle / transmembrane transporter binding / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin ...Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
: / Serotransferrin / Transferrin receptor subunit ESAG6 / Transferrin receptor subunit ESAG7
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsTrevor, C. / Carrington, M. / Higgins, M.K.
Funding support4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/R001138/1
Biotechnology and Biological Sciences Research Council
Wellcome Trust
Engineering and Physical Sciences Research CouncilNS/A000059/1
CitationJournal: Nat Microbiol / Year: 2019
Title: Structure of the trypanosome transferrin receptor reveals mechanisms of ligand recognition and immune evasion.
Authors: Trevor, C.E. / Gonzalez-Munoz, A.L. / Macleod, O.J.S. / Woodcock, P.G. / Rust, S. / Vaughan, T.J. / Garman, E.F. / Minter, R. / Carrington, M. / Higgins, M.K.
History
DepositionAug 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESAG6, subunit of heterodimeric transferrin receptor
B: ESAG7, subunit of heterodimeric transferrin receptor
C: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,9365
Polymers156,6593
Non-polymers2772
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-55 kcal/mol
Surface area51520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.490, 108.110, 115.000
Angle α, β, γ (deg.)90.000, 128.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein ESAG6, subunit of heterodimeric transferrin receptor


Mass: 43898.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: 13J3.10
Production host: Cricetulus longicaudatus (long-tailed hamster)
References: UniProt: Q8WPU1
#2: Protein ESAG7, subunit of heterodimeric transferrin receptor


Mass: 37671.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: 13J3.09
Production host: Cricetulus longicaudatus (long-tailed hamster)
References: UniProt: Q8WPU2
#3: Protein Serotransferrin / Transferrin / Beta-1 metal-binding globulin / Siderophilin


Mass: 75088.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF, PRO1400 / Production host: Homo sapiens (human) / References: UniProt: P02787

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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, 39 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12% (w/v) PEG 5000 MME, 12% 2-methyl-2,4-pentanediol, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→46.3 Å / Num. obs: 40238 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.991 / Net I/σ(I): 9.1
Reflection shellResolution: 2.75→2.8 Å / Num. unique obs: 2045 / CC1/2: 0.553

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→40.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 35.699 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.195 / SU Rfree Blow DPI: 0.309 / SU Rfree Cruickshank DPI: 0.32
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2014 5.01 %RANDOM
Rwork0.183 ---
obs0.185 40234 98.9 %-
Displacement parametersBiso max: 176.52 Å2 / Biso mean: 79 Å2 / Biso min: 35.57 Å2
Baniso -1Baniso -2Baniso -3
1--11.2166 Å20 Å20.8912 Å2
2--9.2107 Å20 Å2
3---2.0059 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.75→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10005 0 15 38 10058
Biso mean--140.37 66.58 -
Num. residues----1288
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3623SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1757HARMONIC5
X-RAY DIFFRACTIONt_it10227HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1303SEMIHARMONIC5
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_contact11366SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10227HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13810HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion23.38
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2674 154 5.11 %
Rwork0.2314 2858 -
all-3012 -
obs--99.6 %
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)
10.5776-0.17370.58260.62920.39911.89180.0219-0.2049-0.1028-0.0250.076-0.02030.09150.1634-0.098-0.1141-0.05430.0209-0.09820.0097-0.0569106.661176.4905-10.6505
20.37290.04080.19341.03640.18641.2538-0.0181-0.27660.1175-0.02460.01060.0382-0.3186-0.04920.0075-0.1075-0.06090.0332-0.1586-0.074-0.039296.481292.0499-8.1829
30.9158-0.17870.34260.61330.1220.0980.09060.1971-0.0622-0.2549-0.07350.0263-0.01550.02-0.01720.12010.0696-0.0084-0.26520.045-0.090376.208190.7305-63.5207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A20 - 342
2X-RAY DIFFRACTION2{ B|* }B18 - 337
3X-RAY DIFFRACTION3{ C|* }C3 - 679

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