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

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ID or keywords:

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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: To Be Published
Title: The Low Density Lipoprotein Receptor LDLR Mediates Cellular Entry of Nonenveloped Hepatitis A Virus
Authors: Stuart DI / Lemon SM
History
DepositionNov 20, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 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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