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- PDB-9nau: CryoEM structure of capsid from human astrovirus 1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9nau
TitleCryoEM structure of capsid from human astrovirus 1 in complex with human neonatal Fc receptor
ComponentsCapsid polyprotein VP70
KeywordsVIRUS / capsid protein / shell domain / VP90 / ORF2 / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


T=3 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host extracellular space
Similarity search - Function
Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Viral coat protein subunit
Similarity search - Domain/homology
: / Capsid polyprotein VP90
Similarity search - Component
Biological speciesHuman astrovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsHall, P.D. / Nelson, C.A. / Fremont, D.H. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI106688 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32DK077653 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of human astrovirus in complex with the neonatal Fc receptor
Authors: Hall, P.D. / Nelson, C.A. / Adams, L.J. / Harshad, I. / Molleston, J.M. / Bui, D. / Baldridge, M.T. / Fremont, D.H.
History
DepositionFeb 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 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: Capsid polyprotein VP70
B: Capsid polyprotein VP70
C: Capsid polyprotein VP70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5614
Polymers135,5223
Non-polymers391
Water00
1
A: Capsid polyprotein VP70
B: Capsid polyprotein VP70
C: Capsid polyprotein VP70
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,133,647240
Polymers8,131,301180
Non-polymers2,34660
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid polyprotein VP70
B: Capsid polyprotein VP70
C: Capsid polyprotein VP70
hetero molecules
x 5


  • icosahedral pentamer
  • 678 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)677,80420
Polymers677,60815
Non-polymers1955
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid polyprotein VP70
B: Capsid polyprotein VP70
C: Capsid polyprotein VP70
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 813 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)813,36524
Polymers813,13018
Non-polymers2356
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid polyprotein VP70


Mass: 45173.895 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: Viral capsid protein deletions caused by trypsin protease during maturation.
Source: (natural) Human astrovirus 1 / Strain: reference strain / References: UniProt: O12792
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
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: Human astrovirus 1 / Type: VIRUS / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Human astrovirus 1 / Strain: reference strain
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: ORF2 / Diameter: 350 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 2200 nm / Nominal defocus min: 1000 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1147.8FEI FALCON IV (4k x 4k)
2145FEI FALCON IV (4k x 4k)
3154.9FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8290 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5EWN

5ewn


Pdb chain-ID: A / Accession code: 5EWN / Chain residue range: 80-411 / Pdb chain residue range: 80-411 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 58.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00297662
ELECTRON MICROSCOPYf_angle_d0.53410455
ELECTRON MICROSCOPYf_chiral_restr0.04411225
ELECTRON MICROSCOPYf_plane_restr0.00531325
ELECTRON MICROSCOPYf_dihedral_angle_d4.47531035

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