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- EMDB-9687: Cryo-EM structure of Echovirus 6 complexed with its uncoating rec... -

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Basic information

Entry
Database: EMDB / ID: EMD-9687
TitleCryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Map dataCryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at ph 7.4
Sample
  • Complex: Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: IgG receptor FcRn large subunit p51
    • Protein or peptide: Beta-2-microglobulinBeta-2 microglobulin
  • Ligand: SPHINGOSINE
  • Ligand: POTASSIUM IONPotassium
  • Ligand: SODIUM IONSodium
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesEchovirus E6 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao GF / Liu S / Zhao X / Peng R
Funding support China, 1 items
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, 2018-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ilm
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ilm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9687.png

Downloads & links

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Map

FileDownload / File: emd_9687.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at ph 7.4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.097 / Movie #1: 0.06
Minimum - Maximum-0.19409378 - 0.31763908
Average (Standard dev.)0.0016758248 (±0.017399272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1940.3180.002

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of Echovirus 6 complexed with its uncoating rec...

EntireName: Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Components
  • Complex: Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: IgG receptor FcRn large subunit p51
    • Protein or peptide: Beta-2-microglobulinBeta-2 microglobulin
  • Ligand: SPHINGOSINE
  • Ligand: POTASSIUM IONPotassium
  • Ligand: SODIUM IONSodium

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Supramolecule #1: Cryo-EM structure of Echovirus 6 complexed with its uncoating rec...

SupramoleculeName: Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Echovirus E6

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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: Echovirus E6
Molecular weightTheoretical: 32.968648 KDa
SequenceString: NDVQNAIDRA VVRVADTMPS GPSNSESIPA LTAAETGHTS QVVPSDTIQT RHVRNFHVRS ESSVENFLSR SACVYIVEYK TRDDTPDKM YDSWVINTRQ VAQLRRKLEF FTYVRFDVEV TFVITSVQDD STRQNTDTPA LTHQIMYVPP GGPIPQAVDD Y NWQTSTNP ...String:
NDVQNAIDRA VVRVADTMPS GPSNSESIPA LTAAETGHTS QVVPSDTIQT RHVRNFHVRS ESSVENFLSR SACVYIVEYK TRDDTPDKM YDSWVINTRQ VAQLRRKLEF FTYVRFDVEV TFVITSVQDD STRQNTDTPA LTHQIMYVPP GGPIPQAVDD Y NWQTSTNP SVFWTEGNAP PRMSIPFMSV GNAYSNFYDG WSHFSQTGVY GFNTLNNMGK LYFRHVNDKT ISPITSKVRI YF KPKHVKA WVPRPPRLCE YTHKDNVDFE PKGVTTSRTQ LTISNSTHVE NY

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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: Echovirus E6
Molecular weightTheoretical: 28.06452 KDa
SequenceString: SDRVRSITLG NSTITTQESA NVVVGYGVWP DYLSDEEATA EDQPTQPDVA TCRFYTLDSV SWMKESQGWW WKFPDALRDM GLFGQNMQY HYLGRSGYTI HVQCNASKFH QGCLLVVCVP EAEMGAANIN EKINREHLSN GEVANTFSGT KSSNTNDVQQ A VFNAGMGV ...String:
SDRVRSITLG NSTITTQESA NVVVGYGVWP DYLSDEEATA EDQPTQPDVA TCRFYTLDSV SWMKESQGWW WKFPDALRDM GLFGQNMQY HYLGRSGYTI HVQCNASKFH QGCLLVVCVP EAEMGAANIN EKINREHLSN GEVANTFSGT KSSNTNDVQQ A VFNAGMGV AVGNLTIFPH QWINLRTNNC ATIVMPYINS VPMDNMFRHY NFTLMIIPFA KLDYAAGSST YIPITVTVAP MC AEYNGLR LAGHQ

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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: Echovirus E6
Molecular weightTheoretical: 26.378936 KDa
SequenceString: GLPVMNTPGS NQFLTSDDYQ SPTAMPQFDV TPEMNIPGEV KNLMEIAEVD SVVPVNNVNE NVNSLEAYRI PVHSVTETGA QVFGFTLQP GADTVMERTL LGEILNYYAN WSGSIKLTFM YCGSAMATGK FLLAYSPPGA GVPKNRREAM LGTHIIWDIG L QSSCVLCV ...String:
GLPVMNTPGS NQFLTSDDYQ SPTAMPQFDV TPEMNIPGEV KNLMEIAEVD SVVPVNNVNE NVNSLEAYRI PVHSVTETGA QVFGFTLQP GADTVMERTL LGEILNYYAN WSGSIKLTFM YCGSAMATGK FLLAYSPPGA GVPKNRREAM LGTHIIWDIG L QSSCVLCV PWISQTHYRF VSKDIYTDAG FITCWYQTSI VVPAEVQNQS VILCFVSACN DFSVRLLRDS PFVRQTAFYQ

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Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E6
Molecular weightTheoretical: 7.338014 KDa
SequenceString:
GAQVSTQKTG AHETSLSASG NSIIHYTNIN YYKDAASNSA NRQDFTQDPG KFTEPVKDIM VKSLPALN

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Macromolecule #5: IgG receptor FcRn large subunit p51

MacromoleculeName: IgG receptor FcRn large subunit p51 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.294971 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LSLLYHLTAV SSPAPGTPAF WVSGWLGPQQ YLSYNSLRGE AEPCGAWVWE NQVSWYWEKE TTDLRIKEKL FLEAFKALGG KGPYTLQGL LGCELGPDNT SVPTAKFALN GEEFMNFDLK QGTWGGDWPE ALAISQRWQQ QDKAANKELT FLLFSCPHRL R EHLERGRG ...String:
LSLLYHLTAV SSPAPGTPAF WVSGWLGPQQ YLSYNSLRGE AEPCGAWVWE NQVSWYWEKE TTDLRIKEKL FLEAFKALGG KGPYTLQGL LGCELGPDNT SVPTAKFALN GEEFMNFDLK QGTWGGDWPE ALAISQRWQQ QDKAANKELT FLLFSCPHRL R EHLERGRG NLEWKEPPSM RLKARPSSPG FSVLTCSAFS FYPPELQLRF LRNGLAAGTG QGDFGPNSDG SFHASSSLTV KS GDEHHYC CIVQHAGLAQ PLRVEL

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Macromolecule #6: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 6 / Number of copies: 1 / 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

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Macromolecule #7: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE / Sphingosine

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Macromolecule #8: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #9: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 9 / Number of copies: 1
Molecular weightTheoretical: 22.99 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 / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26153
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6ilm:
Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4

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