11RN | pdb_000011rn

Complex of B19V VP1u RBD and human transferrin receptor ectodomain

• PDB DOI: https://doi.org/10.2210/pdb11RN/pdb
• EM Map EMD-75980: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Human parvovirus B19
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2026-03-10 Released: 2026-05-27 
• Deposition Author(s): Lee, H., Ros, C., Hafenstein, S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Transferrin receptor 1 binds human parvovirus B19 VP1u to facilitate entry.

Lee, H., Bieri, J., Ammann, N., Suter, C., Hunziker, D., Singh, A.K., Bator, C.M., Hafenstein, S.L., Ros, C.

(2026) Nat Commun 

• PubMed: 42277060 
• DOI: https://doi.org/10.1038/s41467-026-74283-7
• Primary Citation Related Structures: 
  11QC, 11RN


• PubMed 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 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.

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Organizational Affiliation: 
• The Hormel Institute, University of Minnesota, Austin, MN, USA.
Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
Graduate School for Cellular and Biomedical Sciences, Bern, Switzerland.
The Hormel Institute, University of Minnesota, Austin, MN, USA. [e-mail].
Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, MN, USA. [e-mail].
Department of Infectious Disease, Mayo Clinic, Rochester, MN, USA. [e-mail].
Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 158.73 kDa 
• Atom Count: 11,200 
• Modeled Residue Count: 1,398 
• Deposited Residue Count: 1,398 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transferrin receptor protein 1, serum form	A, B	637	Homo sapiens	Mutation(s): 0  Gene Names: TFRC
UniProt & NIH Common Fund Data Resources
Find proteins for P02786 (Homo sapiens) Explore P02786  Go to UniProtKB:  P02786
PHAROS:  P02786 GTEx:  ENSG00000072274
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P02786-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1 structural protein	C [auth X], D [auth Y]	62	Human parvovirus B19	Mutation(s): 0  Gene Names: VP1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_5316
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Lee, H., Ros, C., Hafenstein, S.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release
  
• Version 1.1: 2026-06-24
  Changes: Data collection, Database references