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- PDB-6soz: Glycosylated Trypanosoma brucei transferrin receptor in complex w... -

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Basic information

Entry
Database: PDB / ID: 6soz
TitleGlycosylated Trypanosoma 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


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 / clathrin-coated pit / positive regulation of phosphorylation ...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 / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / actin filament organization / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of protein stability / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Cargo recognition for clathrin-mediated endocytosis / late endosome / Platelet degranulation / Clathrin-mediated endocytosis / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / 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 / ESAG6, subunit of heterodimeric transferrin receptor / ESAG7, subunit of heterodimeric transferrin receptor
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.pdbx_value_order / _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
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)159,19711
Polymers156,6593
Non-polymers2,5388
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14440 Å2
ΔGint-12 kcal/mol
Surface area51180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.180, 117.870, 134.550
Angle α, β, γ (deg.)90.000, 111.450, 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 , 3 types, 7 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 , 1 types, 1 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

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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: 3.3 Å3/Da / Density % sol: 62.7 %
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: 3.42→39.6 Å / Num. obs: 25075 / % possible obs: 99 % / Redundancy: 3.3 % / CC1/2: 0.988 / Net I/σ(I): 11.6
Reflection shellResolution: 3.42→3.48 Å / Num. unique obs: 1291 / CC1/2: 0.692

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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: 3.42→39.59 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.506
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1239 4.94 %RANDOM
Rwork0.211 ---
obs0.212 25066 99 %-
Displacement parametersBiso max: 297.17 Å2 / Biso mean: 216.96 Å2 / Biso min: 118.49 Å2
Baniso -1Baniso -2Baniso -3
1-65.6813 Å20 Å2-31.3159 Å2
2---11.5315 Å20 Å2
3----54.1497 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: final / Resolution: 3.42→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10048 0 162 0 10210
Biso mean--221.51 --
Num. residues----1294
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3737SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1789HARMONIC5
X-RAY DIFFRACTIONt_it10440HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1364SEMIHARMONIC5
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_contact11661SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10440HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14119HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion23.42
LS refinement shellResolution: 3.42→3.56 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2605 132 4.62 %
Rwork0.2589 2726 -
all-2858 -
obs--99.31 %
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)
17.3932-1.2195-1.66621.27440.47490.96310.37250.66890.8614-0.5447-0.2104-0.359-0.1188-0.5233-0.1621-0.19090.272-0.0313-0.18680.139-0.123536.2206-16.313-84.4123
210.0152-0.4555-2.08331.57230.25370.69470.49580.0808-0.9104-0.0241-0.27520.06150.1422-0.2058-0.22060.1230.1474-0.35660.2146-0.1855-0.002641.2402-33.9551-83.6333
311.05881.2937-1.39930.94160.88565.13980.40051.41111.4407-0.7442-0.0431-0.7258-0.7363-0.615-0.3575-0.07950.30560.306-0.19370.05340.15594.5143-18.3779-104.6162
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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