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- PDB-11qc: Human transferrin receptor ectodomain -

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Basic information

Entry
Database: PDB / ID: 11qc
TitleHuman transferrin receptor ectodomain
ComponentsTransferrin receptor protein 1, serum form
KeywordsMEMBRANE PROTEIN / TfR
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 / RHOB GTPase cycle / response to copper ion / RHOJ GTPase cycle / RHOC GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / RHOH GTPase cycle / RAC3 GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / response to retinoic acid / regulation of postsynaptic membrane neurotransmitter receptor levels / transport across blood-brain barrier / positive regulation of B cell proliferation / RAC1 GTPase cycle / clathrin-coated pit / osteoclast differentiation / response to nutrient / positive regulation of T cell proliferation / receptor-mediated endocytosis / Hsp70 protein binding / acute-phase response / iron ion transport / clathrin-coated endocytic vesicle membrane / HFE-transferrin receptor complex / transferrin transport / receptor internalization / positive regulation of protein-containing complex assembly / cellular response to xenobiotic stimulus / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome / recycling endosome membrane / melanosome / Cargo recognition for clathrin-mediated endocytosis / double-stranded RNA binding / Clathrin-mediated endocytosis / extracellular vesicle / virus receptor activity / cytoplasmic vesicle / blood microparticle / basolateral plasma membrane / intracellular iron ion homeostasis / response to hypoxia / early endosome / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / lysosome / endosome / endosome membrane / intracellular signal transduction / external side of plasma membrane / 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 / : / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / 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 / PA domain superfamily / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLee, H. / Ros, C. / Hafenstein, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2026
Title: Transferrin receptor 1 binds human parvovirus B19 VP1u to facilitate entry.
Authors: Hyunwook Lee / Jan Bieri / Nicolas Ammann / Corinne Suter / Daniela Hunziker / Ajit K Singh / Carol M Bator / Susan L Hafenstein / Carlos Ros /
Abstract: Human parvovirus B19 (B19V) displays a strict tropism for erythroid progenitor cells, which is governed by the VP1 unique domain (VP1u). This domain mediates cell-specific uptake through interaction ...Human parvovirus B19 (B19V) displays a strict tropism for erythroid progenitor cells, which is governed by the VP1 unique domain (VP1u). This domain mediates cell-specific uptake through interaction with an unknown cellular receptor, termed VP1uR. Proximity labeling in permissive erythroid cells identifies transferrin receptor 1 (TfR1/CD71) as a predominant membrane protein associated with VP1u. VP1u constructs colocalize with TfR1 at the cell surface of erythroid cells. Incubation with anti-TfR1 antibody OKT9 abolishes binding and uptake of recombinant VP1u. While OKT9 efficiently inhibits B19V uptake and infection, it does not block virus binding to host cells. Direct binding assays confirm interaction of VP1u with human TfR1. Using cryo-EM we solved the 2.4 Å structure of the TfR1-VP1u complex, mapping the binding site. These findings establish TfR1 as the previously unknown receptor, VP1uR, required for B19V uptake.
History
DepositionMar 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)144,5678
Polymers143,2402
Non-polymers1,3276
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 71620.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Production host: Homo sapiens (human) / References: UniProt: P02786
#2: 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.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transferrin receptor 1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIXdev_5316model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 337316 / Symmetry type: POINT

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