[English] 日本語
Yorodumi
- EMDB-49204: CryoEM structure of human astrovirus 1 spike in complex with huma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49204
TitleCryoEM structure of human astrovirus 1 spike in complex with human neonatal Fc receptor
Map datastructure of human astrovirus 1 spike in complex with human neonatal Fc receptor
Sample
  • Virus: Human astrovirus 1
    • Protein or peptide: Capsid polyprotein VP90
    • Protein or peptide: Capsid polyprotein VP70
    • Protein or peptide: IgG receptor FcRn large subunit p51
    • Protein or peptide: Beta-2-microglobulin
Keywordsspike protein / FcRn / FCGRT / VP90 / ORF2 / VIRUS / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / VIRAL PROTEIN
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / T=3 icosahedral viral capsid / IgG binding / beta-2-microglobulin binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / T=3 icosahedral viral capsid / IgG binding / beta-2-microglobulin binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / host extracellular region / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein ...Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Viral coat protein subunit / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Capsid polyprotein VP90 / Capsid polyprotein VP90 / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human) / Human astrovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 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

-
Structure visualization

Supplemental images

emd_49204.png

Downloads & links

-
Map

FileDownload / File: emd_49204.map.gz / Format: CCP4 / Size: 41.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of human astrovirus 1 spike 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 222 pix.
= 246.468 Å		1.11 Å/pix.
x 222 pix.
= 246.468 Å		1.11 Å/pix.
x 222 pix.
= 246.468 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: 0.06
Minimum - Maximum-0.2958807 - 0.43773767
Average (Standard dev.)0.002049201 (±0.026383672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions222222222
Spacing222222222
CellA=B=C: 246.46796 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map B

Fileemd_49204_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_49204_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human astrovirus 1

EntireName: Human astrovirus 1
Components
  • Virus: Human astrovirus 1
    • Protein or peptide: Capsid polyprotein VP90
    • Protein or peptide: Capsid polyprotein VP70
    • Protein or peptide: IgG receptor FcRn large subunit p51
    • Protein or peptide: Beta-2-microglobulin

-
Supramolecule #1: Human astrovirus 1

SupramoleculeName: Human astrovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #3-#4, #1-#2 / 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

-
Macromolecule #1: IgG receptor FcRn large subunit p51

MacromoleculeName: IgG receptor FcRn large subunit p51 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.720383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AESHLSLLYH LTAVSSPAPG TPAFWVSGWL GPQQYLSYNS LRGEAEPCGA WVWENQVSWY WEKETTDLRI KEKLFLEAFK ALGGKGPYT LQGLLGCELG PDNTSVPTAK FALNGEEFMN FDLKQGTWGG DWPEALAISQ RWQQQDKAAN KELTFLLFSC P HRLREHLE ...String:
AESHLSLLYH LTAVSSPAPG TPAFWVSGWL GPQQYLSYNS LRGEAEPCGA WVWENQVSWY WEKETTDLRI KEKLFLEAFK ALGGKGPYT LQGLLGCELG PDNTSVPTAK FALNGEEFMN FDLKQGTWGG DWPEALAISQ RWQQQDKAAN KELTFLLFSC P HRLREHLE RGRGNLEWKE PPSMRLKARP SSPGFSVLTC SAFSFYPPEL QLRFLRNGLA AGTGQGDFGP NSDGSFHASS SL TVKSGDE HHYCCIVQHA GLAQPLRVEL

UniProtKB: IgG receptor FcRn large subunit p51

-
Macromolecule #2: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.74816 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQRTPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTEF TPTEKDEYAC RVNHVTLSQ PKIVKWDRDM

UniProtKB: Beta-2-microglobulin

-
Macromolecule #3: Capsid polyprotein VP90

MacromoleculeName: Capsid polyprotein VP90 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human astrovirus 1
Molecular weightTheoretical: 70.095953 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 EAPAAFGRSI PAPGEEFKVV LTFGSPMSPN ANNKQTWVNK SLDAPSGHYN VKIAKDVDHY LTMQG FTSI ASVDWYTTDF QPSEAPAPIQ GLQVLVNISK KADVYAVKQF VTAQTNNKHQ VTSLFLVKVT TGFQVNNYLS YFYRAS ATG DATTNLLVRG DTYTAGISFT QGGWYLLTNT SIVDGAMPPG WVWNNVELKT NTAYHMDKGL VHLIMPLPES TQMCYEM LT SI

UniProtKB: Capsid polyprotein VP90

-
Macromolecule #4: Capsid polyprotein VP70

MacromoleculeName: Capsid polyprotein VP70 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human astrovirus 1
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
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

+
Image processing

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

5ewo

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54839
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

5ewn

chain_id: A, residue_range: 80-411, source_name: PDB, initial_model_type: experimental model

5ewo

source_name: PDB, initial_model_type: experimental model

1exu

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9nav:
CryoEM structure of human astrovirus 1 spike in complex with human neonatal Fc receptor

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more