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- EMDB-55772: Hepatitis A Virus in complex with GD1a -

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Basic information

Entry
Database: EMDB / ID: EMD-55772
TitleHepatitis A Virus in complex with GD1a
Map dataHAV in complex with GD1a
Sample
  • Virus: Human hepatitis A virus
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
  • Ligand: water
KeywordsHepatitis A Virus GD1a / VIRUS
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / symbiont entry into host cell / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus ...Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman hepatitis A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 1.7 Å
AuthorsZhao Y / Stuart D / Lemon SM / Duyvesteyn H / Shah P / Fry E
Funding support United States, United Kingdom, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01- 438 AI103083 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)01-AI131685 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-AI150095 United States
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: The low-density lipoprotein receptor LDLR mediates cellular entry of nonenveloped hepatitis A virus.
Authors: Tomoyuki Shiota / Yuguang Zhao / Itoe Shiota / Helen M E Duyvesteyn / Manami Yamaoka / Anshuman Das / Maryna Kapustina / Pranav Shah / Masamichi Muramatsu / Xiangxi Wang / Elizabeth E Fry / ...Authors: Tomoyuki Shiota / Yuguang Zhao / Itoe Shiota / Helen M E Duyvesteyn / Manami Yamaoka / Anshuman Das / Maryna Kapustina / Pranav Shah / Masamichi Muramatsu / Xiangxi Wang / Elizabeth E Fry / David I Stuart / Stanley M Lemon /
Abstract: Hepatitis A virus (HAV) is an unusual picornavirus with two types of extracellular virions: nonenveloped particles (nHAV) shed in feces and quasi-enveloped particles (eHAV) circulating in blood. Both ...Hepatitis A virus (HAV) is an unusual picornavirus with two types of extracellular virions: nonenveloped particles (nHAV) shed in feces and quasi-enveloped particles (eHAV) circulating in blood. Both enter cells by clathrin-dependent endocytic pathways merging in late endolysosomes with capsid binding to ganglioside receptors. Phosphatidylserine receptors facilitate eHAV endocytosis, but no protein receptor has been identified for nHAV. Here, we show low-density lipoprotein receptor (LDLR) is such a receptor. LDLR knockout did not alter viral attachment to cells, but restricted cellular uptake of nHAV (not eHAV). Soluble LDLR ectodomain blocked nHAV entry, as did antibody to LDLR. Recombinant LDLR-related protein-associated protein 1, a pan-LDLR family chaperone, also inhibited nHAV entry, including residual entry into knockout cells, suggesting other LDLR family members may similarly facilitate endocytosis. Reconstituting full-length LDLR expression restored nHAV entry in knockout cells, whereas LDLR mutants lacking LA repeats 4 to 7 or the EGF-like/propeller domain did not. ELISAs confirmed LDLR binds nHAV, optimally above pH7, without destabilizing the capsid. A 1.7Å resolution cryoelectron microscopy (cryo-EM) structure revealed LDLR interacts with VP1 at the fivefold vertex of the capsid. Extreme blurring of the LDLR density prevented detailed identification of LDLR interactions, and suggested binding does not follow particle symmetry, being either flexible or to multiple LDLR regions. Additional cryo-EM studies show ganglioside GD1a binds to a similar region of the capsid. Collectively, these data reveal the LDLR to be an important entry factor, shuttling nHAV from the extracellular environment to endolysosomes where it is likely released at low pH to bind gangliosides.
History
DepositionNov 20, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55772.png

Downloads & links

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Map

FileDownload / File: emd_55772.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHAV in complex with GD1a
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 600 pix.
= 438.18 Å		0.73 Å/pix.
x 600 pix.
= 438.18 Å		0.73 Å/pix.
x 600 pix.
= 438.18 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.26992622 - 0.9527493
Average (Standard dev.)0.004885408 (±0.05636529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 438.18 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half B HAV with GD1a

Fileemd_55772_half_map_1.map
AnnotationHalf_B HAV with GD1a
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A HAV with GD1a

Fileemd_55772_half_map_2.map
AnnotationHalf_A HAV with GD1a
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human hepatitis A virus

EntireName: Human hepatitis A virus
Components
  • Virus: Human hepatitis A virus
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
  • Ligand: water

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Supramolecule #1: Human hepatitis A virus

SupramoleculeName: Human hepatitis A virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 208726 / Sci species name: Human hepatitis A virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human hepatitis A virus
Molecular weightTheoretical: 30.244896 KDa
Recombinant expressionOrganism: Chlorocebus aethiops aethiops (mammal)
SequenceString: VGDDSGGFST TVSTEQNVPD PQVGITTMKD LKGKANRGKM DVSGVQAPVG AITTIEDPVL AKKVPETFPE LKPGESRHTS DHMSIYKFM GRSHFLCTFT FNSNNKEYTF PITLSSTSNP PHGLPSTLRW FFNLFQLYRG PLDLTIIITG ATDVDGMAWF T PVGLAVDT ...String:
VGDDSGGFST TVSTEQNVPD PQVGITTMKD LKGKANRGKM DVSGVQAPVG AITTIEDPVL AKKVPETFPE LKPGESRHTS DHMSIYKFM GRSHFLCTFT FNSNNKEYTF PITLSSTSNP PHGLPSTLRW FFNLFQLYRG PLDLTIIITG ATDVDGMAWF T PVGLAVDT PWVEKESALS IDYKTALGAV RFNTRRTGNI QIRLPWYSYL YAVSGALDGL GDKTDSTFGL VSIQIANYNH SD EYLSFSC YLSVTEQSEF YFPRAPLNSN AMLSTES

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human hepatitis A virus
Molecular weightTheoretical: 24.870053 KDa
Recombinant expressionOrganism: Chlorocebus aethiops aethiops (mammal)
SequenceString: DIEEEQMIQS VDRTAVTGAS YFTSVDQSSV HTAEVGSHQV EPLRTSVDKP GSKKTQGEKF FLIHSADWLT THALFHEVAK LDVVKLLYN EQFAVQGLLR YHTYARFGIE IQVQINPTPF QQGGLICAMV PGDQSYGSIA SLTVYPHGLL NCNINNVVRI K VPFIYTRG ...String:
DIEEEQMIQS VDRTAVTGAS YFTSVDQSSV HTAEVGSHQV EPLRTSVDKP GSKKTQGEKF FLIHSADWLT THALFHEVAK LDVVKLLYN EQFAVQGLLR YHTYARFGIE IQVQINPTPF QQGGLICAMV PGDQSYGSIA SLTVYPHGLL NCNINNVVRI K VPFIYTRG AYHFKDPQYP VWELTIRVWS ELNIGTGTSA YTSLNVLARF TDLELHGLTP LSTQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human hepatitis A virus
Molecular weightTheoretical: 27.835693 KDa
Recombinant expressionOrganism: Chlorocebus aethiops aethiops (mammal)
SequenceString: MMRNETRVST TENVVNLSNY EDARAKMSFA LDQEDWKSDP SQGGGIKITH FTTWTSIPTL AAQFPFNASD SVGQQIKVIP VDPYFFQMT NTNPDQKCIT ALASICQMFC FWRGDLVFDF QVFPTKYHSG RLLFCFVPGN ELIDVTGITL KQATTAPCAV M DIAGVQST ...String:
MMRNETRVST TENVVNLSNY EDARAKMSFA LDQEDWKSDP SQGGGIKITH FTTWTSIPTL AAQFPFNASD SVGQQIKVIP VDPYFFQMT NTNPDQKCIT ALASICQMFC FWRGDLVFDF QVFPTKYHSG RLLFCFVPGN ELIDVTGITL KQATTAPCAV M DIAGVQST LRFRVPWISD TPYRVNRYTK EAHQKGEYTA IGKLIVYCYN RLTSPSNVAH HVRVNVYLSA INLECFAPLY HA MDVTTQ

UniProtKB: Genome polyprotein

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 73 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
Component:
ConcentrationFormulaName
10.0 mMHepesHepes
150.0 mMNaClsodium chloride
2.0 mMCaCl2calcium chloride

Details: 10 mM Hepes 150 mM NaCl 2 mM CaCl2
VitrificationCryogen name: ETHANE
DetailsHAV vaccine

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5wte

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 93507
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial modelPDB ID:

5wte


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9tbi:
Hepatitis A Virus in complex with GD1a

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