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- PDB-8p0z: AP01-S2.3 - a variant of a redesigned transferrin receptor apical... -

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Basic information

Entry
Database: PDB / ID: 8p0z
TitleAP01-S2.3 - a variant of a redesigned transferrin receptor apical domain
ComponentsTransferrin receptor protein 1, serum form
KeywordsCYTOSOLIC PROTEIN / receptor domain / transferrin
Function / homology
Function and homology information


transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / positive regulation of isotype switching / Transferrin endocytosis and recycling / response to manganese ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / RND1 GTPase cycle / RND2 GTPase cycle ...transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / positive regulation of isotype switching / Transferrin endocytosis and recycling / response to manganese ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / RND1 GTPase cycle / RND2 GTPase cycle / response to copper ion / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / response to retinoic acid / regulation of postsynaptic membrane neurotransmitter receptor levels / transport across blood-brain barrier / clathrin-coated pit / positive regulation of B cell proliferation / Hsp70 protein binding / positive regulation of T cell proliferation / response to nutrient / RAC1 GTPase cycle / osteoclast differentiation / cellular response to leukemia inhibitory factor / transferrin transport / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / iron ion transport / HFE-transferrin receptor complex / recycling endosome / receptor internalization / multicellular organismal-level iron ion homeostasis / positive regulation of protein localization to nucleus / cellular response to xenobiotic stimulus / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / melanosome / extracellular vesicle / double-stranded RNA binding / virus receptor activity / cytoplasmic vesicle / blood microparticle / basolateral plasma membrane / intracellular iron ion homeostasis / response to hypoxia / early endosome / endosome membrane / positive regulation of canonical NF-kappaB signal transduction / endosome / intracellular signal transduction / external side of plasma membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
BORIC ACID / Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsOberdorfer, G. / Grill, B. / Bjelic, S. / Stoll, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)802217European Union
CitationJournal: J.Mol.Biol. / Year: 2023
Title: Affinity Maturated Transferrin Receptor Apical Domain Blocks Machupo Virus Glycoprotein Binding.
Authors: Sjostrom, D.J. / Grill, B. / Ambrosetti, E. / Veetil, A.A. / Mohlin, C. / Teixeira, A.I. / Oberdofer, G. / Bjelic, S.
History
DepositionMay 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transferrin receptor protein 1, serum form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2884
Polymers18,1811
Non-polymers1083
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-21 kcal/mol
Surface area7980 Å2
Unit cell
Length a, b, c (Å)32.990, 57.370, 39.100
Angle α, β, γ (deg.)90.000, 113.152, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Transferrin receptor protein 1, serum form / sTfR


Mass: 18180.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* (DE3) / References: UniProt: P02786
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.87 Å3/Da / Density % sol: 34.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 11 mg/mL protein in 20 mM HEPES, pH 6.8, 150 mM NaCl mixed with 100 mM MIB buffer, pH 7.5, and 24 % PEG in a ratio 1:2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.88→35.95 Å / Num. obs: 10690 / % possible obs: 97.06 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.96 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.1036 / Rrim(I) all: 0.2192 / Net I/σ(I): 5.72
Reflection shellResolution: 1.88→1.947 Å / Rmerge(I) obs: 1.189 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 1053 / CC1/2: 0.522 / CC star: 0.828 / Rpim(I) all: 0.6386 / Rrim(I) all: 1.356 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3777refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→35.95 Å / SU ML: 0.2548 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.3042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 535 5.02 %random selection
Rwork0.2134 10130 --
obs0.2143 10664 97.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.35 Å2
Refinement stepCycle: LAST / Resolution: 1.88→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 6 108 1290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031290
X-RAY DIFFRACTIONf_angle_d0.64671751
X-RAY DIFFRACTIONf_chiral_restr0.0495203
X-RAY DIFFRACTIONf_plane_restr0.0025229
X-RAY DIFFRACTIONf_dihedral_angle_d13.4463484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-2.070.32861320.3282497X-RAY DIFFRACTION95.84
2.07-2.370.2841330.25432511X-RAY DIFFRACTION97.35
2.37-2.980.2411330.22822534X-RAY DIFFRACTION97.23
2.98-35.950.20671370.17872588X-RAY DIFFRACTION97.92

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