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- EMDB-49203: CryoEM structure of capsid from human astrovirus 1 in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-49203
TitleCryoEM structure of capsid from human astrovirus 1 in complex with human neonatal Fc receptor
Map dataCryoEM structure of capsid from human astrovirus 1 in complex with human neonatal Fc receptor
Sample
  • Virus: Human astrovirus 1
    • Protein or peptide: Capsid polyprotein VP70
  • Ligand: POTASSIUM ION
Keywordscapsid protein / shell domain / VP90 / ORF2 / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / VIRUS
Function / homologyTurkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / host extracellular space / Capsid polyprotein VP90
Function and homology information
Biological speciesHuman astrovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsHall PD / Nelson CA / Fremont DH / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 3 items
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 PD / Nelson CA / Adams LJ / Harshad I / Molleston JM / Bui D / Baldridge MT / Fremont DH
History
DepositionFeb 12, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49203.png

Downloads & links

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Map

FileDownload / File: emd_49203.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of capsid from human astrovirus 1 in complex with human neonatal Fc receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 666 pix.
= 739.404 Å		1.11 Å/pix.
x 666 pix.
= 739.404 Å		1.11 Å/pix.
x 666 pix.
= 739.404 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11022 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.11637566 - 0.2600648
Average (Standard dev.)-0.0001850676 (±0.0112695675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions666666666
Spacing666666666
CellA=B=C: 739.40393 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_49203_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49203_half_map_2.map
AnnotationHalf Map A
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 astrovirus 1

EntireName: Human astrovirus 1
Components
  • Virus: Human astrovirus 1
    • Protein or peptide: Capsid polyprotein VP70
  • Ligand: POTASSIUM ION

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Supramolecule #1: Human astrovirus 1

SupramoleculeName: Human astrovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 12456 / Sci species name: Human astrovirus 1 / Sci species strain: reference strain / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: ORF2 / Diameter: 350.0 Å / T number (triangulation number): 3

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Macromolecule #1: Capsid polyprotein VP70

MacromoleculeName: Capsid polyprotein VP70 / type: protein_or_peptide / ID: 1
Details: Viral capsid protein deletions caused by trypsin protease during maturation.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human astrovirus 1 / Strain: reference strain
Molecular weightTheoretical: 45.173895 KDa
SequenceString: MASKSNKQVT VEVSNNGRNR SKSRARSQSR GRDKSVKITV NSRNRARRQP GRDKRQSSQR VRNIVNKQLR KQGVTGPKPA ICQRATATL GTVGSNTSGT TEIEACILLN PVLVKDATGS TQFGPVQALG AQYSMWKLKY LNVKLTSMVG ASAVNGTVLR V SLNPTSTP ...String:
MASKSNKQVT VEVSNNGRNR SKSRARSQSR GRDKSVKITV NSRNRARRQP GRDKRQSSQR VRNIVNKQLR KQGVTGPKPA ICQRATATL GTVGSNTSGT TEIEACILLN PVLVKDATGS TQFGPVQALG AQYSMWKLKY LNVKLTSMVG ASAVNGTVLR V SLNPTSTP SSTSWSGLGA RKHLDVTVGK NATFKLKPSD LGGPRDGWWL TNTNDNASDT LGPSIEIHTL GRTMSSYKNE QF TGGLFLV ELASEWCFTG YAANPNLVNL VKSTDNQVPV TFEGSAGSPL IMNVPEGSHF ARTVLARSTT PTTLARAGER TTS DTVWQV LNTAVSAAEL VTPPPFNWLV KGGWWFVKLI AGRTRTGSRS FYVYPSYQDA LSNKPALCTG STPGGMRTRN PVTT TLQFT QMNQPSLGHG EAP

UniProtKB: Capsid polyprotein VP90

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON IV (4k x 4k) / #0 - Average electron dose: 47.8 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON IV (4k x 4k) / #1 - Average electron dose: 45.0 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: FEI FALCON IV (4k x 4k) / #2 - Average electron dose: 54.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ewn

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8290
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ewn


Chain - Chain ID: A / Chain - Residue range: 80-411 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9nau:
CryoEM structure of capsid from human astrovirus 1 in complex with human neonatal Fc receptor

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