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- EMDB-30318: E30 F-particle in complex with FcRn -

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Basic information

Entry
Database: EMDB / ID: EMD-30318
TitleE30 F-particle in complex with FcRn
Map data
Sample
  • Complex: Echovirus E30
    • Complex: E30 F-particle in complex with FcRn
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
      • Protein or peptide: VP4
    • Complex: E30 F-particle in complex with FcRn
      • Protein or peptide: IgG receptor FcRn large subunit p51
      • Protein or peptide: Beta-2-microglobulin
  • Ligand: MYRISTIC ACID
KeywordsEchovirus B / mature / receptor / VIRUS
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / peptide antigen assembly with MHC class II protein complex / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / T=pseudo3 icosahedral viral capsid / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / host cell cytoplasmic vesicle membrane / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / viral capsid / tertiary granule lumen / DAP12 signaling / host cell / negative regulation of neuron projection development / nucleoside-triphosphate phosphatase / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / channel activity / protein refolding / early endosome membrane / monoatomic ion transmembrane transport / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / DNA replication / RNA helicase activity / endosome membrane / immune response / symbiont-mediated suppression of host gene expression / endocytosis involved in viral entry into host cell / Amyloid fiber formation / endoplasmic reticulum lumen / symbiont-mediated activation of host autophagy / external side of plasma membrane / Golgi membrane / lysosomal membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity / DNA-templated transcription / Neutrophil degranulation / virion attachment to host cell / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / MHC class I-like antigen recognition-like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / MHC class I-like antigen recognition-like superfamily / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / MHC classes I/II-like antigen recognition protein / Picornavirus/Calicivirus coat 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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin / Genome polyprotein / VP4
Similarity search - Component
Biological speciesEchovirus E30 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang K / Zhu L
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesKJZD-SW-L05 China
CitationJournal: Nat Commun / Year: 2020
Title: Structures of Echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage.
Authors: Kang Wang / Ling Zhu / Yao Sun / Minhao Li / Xin Zhao / Lunbiao Cui / Li Zhang / George F Gao / Weiwei Zhai / Fengcai Zhu / Zihe Rao / Xiangxi Wang /
Abstract: Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor ...Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor usage, among which echovirus 30 (E30), a leading causative agent for human aseptic meningitis, utilizes FcRn as an uncoating receptor. However, receptors for many EVs remain unknown. Here we analyzed the atomic structures of E30 mature virion, empty- and A-particles, which reveals serotype-specific epitopes and striking conformational differences between the subgroups within EV-Bs. Of these, the VP1 BC loop markedly distinguishes E30 from other EV-Bs, indicative of a role as a structural marker for EV-B. By obtaining cryo-electron microscopy structures of E30 in complex with its receptor FcRn and CD55 and comparing its homologs, we deciphered the underlying molecular basis for receptor recognition. Together with experimentally derived viral receptor identifications, we developed a structure-based in silico algorithm to inform a rational prediction for EV receptor usage.
History
DepositionJun 7, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c9v
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7c9v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30318.png

Downloads & links

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Map

FileDownload / File: emd_30318.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 360 pix.
= 473.76 Å		1.32 Å/pix.
x 360 pix.
= 473.76 Å		1.32 Å/pix.
x 360 pix.
= 473.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.316 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.022912886 - 0.049080502
Average (Standard dev.)0.00005494475 (±0.0039325254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 473.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3161.3161.316
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z473.760473.760473.760
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0230.0490.000

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Supplemental data

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Sample components

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Entire : Echovirus E30

EntireName: Echovirus E30
Components
  • Complex: Echovirus E30
    • Complex: E30 F-particle in complex with FcRn
      • Protein or peptide: VP1
      • Protein or peptide: VP2
      • Protein or peptide: VP3
      • Protein or peptide: VP4
    • Complex: E30 F-particle in complex with FcRn
      • Protein or peptide: IgG receptor FcRn large subunit p51
      • Protein or peptide: Beta-2-microglobulin
  • Ligand: MYRISTIC ACID

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Supramolecule #1: Echovirus E30

SupramoleculeName: Echovirus E30 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: Particles purified from the cell cultures innoculated with the live E30.
Source (natural)Organism: Echovirus E30

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Supramolecule #2: E30 F-particle in complex with FcRn

SupramoleculeName: E30 F-particle in complex with FcRn / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4

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Supramolecule #3: E30 F-particle in complex with FcRn

SupramoleculeName: E30 F-particle in complex with FcRn / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E30
Molecular weightTheoretical: 33.091008 KDa
SequenceString: NDPESALNRA VGRVADTVAS GPVNTEQIPA LTAVETGHTS QVVPSDTMQT RHVINYHTRS ESSIENFMGR AACVYIAQYA TEKVNDELD RYTNWEITTR QVAQLRRKLE MFTYMRFDLE ITFVITSSQR TSTTYASDSP PLTHQVMYVP PGGPIPKSYE D FAWQTSTN ...String:
NDPESALNRA VGRVADTVAS GPVNTEQIPA LTAVETGHTS QVVPSDTMQT RHVINYHTRS ESSIENFMGR AACVYIAQYA TEKVNDELD RYTNWEITTR QVAQLRRKLE MFTYMRFDLE ITFVITSSQR TSTTYASDSP PLTHQVMYVP PGGPIPKSYE D FAWQTSTN PSVFWTEGNA PPRMSIPFMS VGNAYCNFYD GWSHFSQSGV YGYTTLNNMG HLYFRHVNKS TAYPVNSVAR VY FKPKHVK AWVPRAPRLC PYLKARNVNF NVQGVTESRN KITLDRSTHN PLANT

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E30
Molecular weightTheoretical: 28.878502 KDa
SequenceString: SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPT YLSDHEATAV DQPTQPDVAT CRFYTLESVK WESSSAGWWW KFPEALSDM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGAATTDH AFNHTKLSNI GQAMEFSAKK S TDQTGPQT ...String:
SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPT YLSDHEATAV DQPTQPDVAT CRFYTLESVK WESSSAGWWW KFPEALSDM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGAATTDH AFNHTKLSNI GQAMEFSAKK S TDQTGPQT AVHNAGMGVA VGNLTIFPHQ WINLRTNNSA TIVMPYINSV PMDNMYRHYN FTLMVIPFAK LEHSPQASTY VP ITVTVAP MCAEYNGLRL AGHQ

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E30
Molecular weightTheoretical: 26.157531 KDa
SequenceString: GLPTMNTPGS TQFLTSDDFQ SPSAMPQFDV TPEIQIPGQV RNLMEIAEVD SVVPVNNTEG HVNSMEAYRI PVRPQTSSGE QVFGFQLQP GHDSVLKHTL LGEILNYYAN WSGSMKLTFM YCGAAMATGK FLIAYSPPGA GVPGSRRDAM LGTHVIWDVG L QSSCVLCV ...String:
GLPTMNTPGS TQFLTSDDFQ SPSAMPQFDV TPEIQIPGQV RNLMEIAEVD SVVPVNNTEG HVNSMEAYRI PVRPQTSSGE QVFGFQLQP GHDSVLKHTL LGEILNYYAN WSGSMKLTFM YCGAAMATGK FLIAYSPPGA GVPGSRRDAM LGTHVIWDVG L QSSCVLCV PWISQTNYRY VTSDAYTDAG YITCWYQTSI VTPPDIPTTS TILCFVSACN DFSVRLLRDT PFITQQALFQ

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E30
Molecular weightTheoretical: 7.437145 KDa
SequenceString:
GAQVSTQKTG AHETGLNASG NSIIHYTNIN YYKDSASNSL NRQDFTQDPS KFTEPVKDVM IKTLPALN

UniProtKB: Genome polyprotein

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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

UniProtKB: IgG receptor FcRn large subunit p51

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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

UniProtKB: Beta-2-microglobulin

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Macromolecule #7: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 7 / Number of copies: 1 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 7299
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7c9v:
E30 F-particle in complex with FcRn

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