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- EMDB-75980: Complex of B19V VP1u RBD and human transferrin receptor ectodomain -

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Basic information

Entry
Database: EMDB / ID: EMD-75980
TitleComplex of B19V VP1u RBD and human transferrin receptor ectodomain
Map dataFlex map of B19V VP1u-TfR complex
Sample
  • Organelle or cellular component: Complex of B19V VP1u RBD and transferrin receptor 1
    • Protein or peptide: Transferrin receptor protein 1, serum form
    • Protein or peptide: VP1 structural protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTfR / B19V / VP1u / RBD / MEMBRANE PROTEIN
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 / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLee H / Ros C / Hafenstein S
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75980.png

Downloads & links

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Map

FileDownload / File: emd_75980.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFlex map of B19V VP1u-TfR complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 400 pix.
= 264. Å		0.66 Å/pix.
x 400 pix.
= 264. Å		0.66 Å/pix.
x 400 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.016941113 - 0.037723374
Average (Standard dev.)0.000051672458 (±0.00091570866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: NU-refinement sharpened map of B19V VP1u-TfR complex

Fileemd_75980_additional_1.map
AnnotationNU-refinement sharpened map of B19V VP1u-TfR complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: NU-refinement unsharpened map of B19V VP1u-TfR complex

Fileemd_75980_additional_2.map
AnnotationNU-refinement unsharpened map of B19V VP1u-TfR complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of B19V VP1u-TfR complex

Fileemd_75980_half_map_1.map
AnnotationHalf map B of B19V VP1u-TfR complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of B19V VP1u-TfR complex

Fileemd_75980_half_map_2.map
AnnotationHalf map A of B19V VP1u-TfR complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of B19V VP1u RBD and transferrin receptor 1

EntireName: Complex of B19V VP1u RBD and transferrin receptor 1
Components
  • Organelle or cellular component: Complex of B19V VP1u RBD and transferrin receptor 1
    • Protein or peptide: Transferrin receptor protein 1, serum form
    • Protein or peptide: VP1 structural protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of B19V VP1u RBD and transferrin receptor 1

SupramoleculeName: Complex of B19V VP1u RBD and transferrin receptor 1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transferrin receptor protein 1, serum form

MacromoleculeName: Transferrin receptor protein 1, serum form / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.34375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LYWDDLKRKL SEKLDSTDFT GTIKLLNENS YVPREAGSQK DENLALYVEN QFREFKLSKV WRDQHFVKIQ VKDSAQNSVI IVDKNGRLV YLVENPGGYV AYSKAATVTG KLVHANFGTK KDFEDLYTPV NGSIVIVRAG KITFAEKVAN AESLNAIGVL I YMDQTKFP ...String:
LYWDDLKRKL SEKLDSTDFT GTIKLLNENS YVPREAGSQK DENLALYVEN QFREFKLSKV WRDQHFVKIQ VKDSAQNSVI IVDKNGRLV YLVENPGGYV AYSKAATVTG KLVHANFGTK KDFEDLYTPV NGSIVIVRAG KITFAEKVAN AESLNAIGVL I YMDQTKFP IVNAELSFFG HAHLGTGDPY TPGFPSFNHT QFPPSRSSGL PNIPVQTISR AAAEKLFGNM EGDCPSDWKT DS TCRMVTS ESKNVKLTVS NVLKEIKILN IFGVIKGFVE PDHYVVVGAQ RDAWGPGAAK SGVGTALLLK LAQMFSDMVL KDG FQPSRS IIFASWSAGD FGSVGATEWL EGYLSSLHLK AFTYINLDKA VLGTSNFKVS ASPLLYTLIE KTMQNVKHPV TGQF LYQDS NWASKVEKLT LDNAAFPFLA YSGIPAVSFC FCEDTDYPYL GTTMDTYKEL IERIPELNKV ARAAAEVAGQ FVIKL THDV ELNLDYERYN SQLLSFVRDL NQYRADIKEM GLSLQWLYSA RGDFFRATSR LTTDFGNAEK TDRFVMKKLN DRVMRV EYH FLSPYVSPKE SPFRHVFWGS GSHTLPALLE NLKLRKQNNG AFNETLFRNQ LALATWTIQG AANALSGDVW DIDN

UniProtKB: Transferrin receptor protein 1

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Macromolecule #2: VP1 structural protein

MacromoleculeName: VP1 structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human parvovirus B19
Molecular weightTheoretical: 7.357111 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
WWESDDEFAK AVYQQFVEFY EKVTGTDLEL IQILKDHYNI SLDNPLENPS SLFDLVARIK NN

UniProtKB: VP1 structural protein

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 613000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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