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- PDB-11rn: Complex of B19V VP1u RBD and human transferrin receptor ectodomain -

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Basic information

Entry
Database: PDB / ID: 11rn
TitleComplex of B19V VP1u RBD and human transferrin receptor ectodomain
Components
  • Transferrin receptor protein 1, serum form
  • VP1 structural protein
KeywordsMEMBRANE PROTEIN / TfR / B19V / VP1u / RBD
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 / Golgi Associated Vesicle Biogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / 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 / response to nutrient / positive regulation of T cell proliferation / osteoclast differentiation / Hsp70 protein binding / receptor-mediated endocytosis / acute-phase response / cellular response to leukemia inhibitory factor / iron ion transport / clathrin-coated endocytic vesicle membrane / HFE-transferrin receptor complex / transferrin transport / positive regulation of protein-containing complex assembly / receptor internalization / multicellular organismal-level iron ion homeostasis / positive regulation of protein localization to nucleus / recycling endosome / cellular response to xenobiotic stimulus / 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 / endosome membrane / endosome / 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 / structural molecule activity / 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 ...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 / Phospholipase A2-like domain / Phospholipase A2-like domain
Similarity search - Domain/homology
VP1 structural protein / Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human parvovirus B19
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: Lee, H. / Bieri, J. / Ammann, N. / Suter, C. / Hunziker, D. / Singh, A.K. / Hafenstein, S.L. / Ros, C.
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
Revision 1.0May 27, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / 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
X: VP1 structural protein
Y: VP1 structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,72910
Polymers157,4024
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: 71343.750 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: Protein VP1 structural protein


Mass: 7357.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parvovirus B19 / Gene: VP1 / Production host: Homo sapiens (human) / References: UniProt: A0A3Q9D3C4
#3: 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: Complex of B19V VP1u RBD and transferrin receptor 1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
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: 613000 / Symmetry type: POINT

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