[English] 日本語
Yorodumi
- PDB-6ilm: Cryo-EM structure of Echovirus 6 complexed with its uncoating rec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ilm
TitleCryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Components
  • (Capsid protein ...) x 4
  • Beta-2-microglobulin
  • IgG receptor FcRn large subunit p51
KeywordsVIRUS / Echovirus 6 / FcRn / Cryo-EM / virus-receptor complex
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / 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 ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / 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 / MHC class II protein complex binding / DAP12 signaling / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / protein refolding / ER-Phagosome pathway / early endosome membrane / 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
Jelly Rolls - #20 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / : ...Jelly Rolls - #20 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / SPHINGOSINE / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Echovirus E6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao, G.F. / Liu, S. / Zhao, X. / Peng, R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010000 China
CitationJournal: Cell / Year: 2019
Title: Human Neonatal Fc Receptor Is the Cellular Uncoating Receptor for Enterovirus B.
Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / ...Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / Yan Li / Meifan Zhang / Jianxun Qi / Han Wang / Ning Du / Yan Wu / Yuhai Bi / Shan Gao / Yi Shi / Jinghua Yan / Yong Zhang / Zhengde Xie / Wensheng Wei / George F Gao /
Abstract: Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for ...Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for coxsackievirus B in EV-B have been identified, receptors mediating virus entry, especially the uncoating process of echovirus and other EV-B remain obscure. Here, we found that human neonatal Fc receptor (FcRn) is the uncoating receptor for major EV-B. FcRn binds to the virus particles in the "canyon" through its FCGRT subunit. By obtaining multiple cryo-electron microscopy structures at different stages of virus entry at atomic or near-atomic resolution, we deciphered the underlying mechanisms of enterovirus attachment and uncoating. These structures revealed that different from the attachment receptor CD55, binding of FcRn to the virions induces efficient release of "pocket factor" under acidic conditions and initiates the conformational changes in viral particle, providing a structural basis for understanding the mechanisms of enterovirus entry.
History
DepositionOct 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.6Jun 25, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-9687
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9687
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,1559
Polymers135,7936
Non-polymers3623
Water00
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,169,290540
Polymers8,147,595360
Non-polymers21,695180
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 protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 5


  • icosahedral pentamer
  • 681 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)680,77445
Polymers678,96630
Non-polymers1,80815
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 817 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)816,92954
Polymers814,75936
Non-polymers2,16918
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))

-
Components

-
Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein Capsid protein VP1


Mass: 32968.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#2: Protein Capsid protein VP2


Mass: 28064.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#3: Protein Capsid protein VP3


Mass: 26378.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#4: Protein Capsid protein VP4


Mass: 7338.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6

-
Protein , 2 types, 2 molecules EF

#5: Protein IgG receptor FcRn large subunit p51 / FcRn / Neonatal Fc receptor


Mass: 29294.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCRN / Cell (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P55899
#6: Protein Beta-2-microglobulin / FcRn light chain


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P61769

-
Non-polymers , 3 types, 3 molecules

#7: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MH830353.1 FOR THE PROTEIN.

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Echovirus E612062
31Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26153 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039789
ELECTRON MICROSCOPYf_angle_d0.75513328
ELECTRON MICROSCOPYf_dihedral_angle_d8.4235786
ELECTRON MICROSCOPYf_chiral_restr0.0521442
ELECTRON MICROSCOPYf_plane_restr0.0071735

+
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