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

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Basic information

Entry
Database: PDB / ID: 7c9v
TitleE30 F-particle in complex with FcRn
Components
  • Beta-2-microglobulin
  • IgG receptor FcRn large subunit p51
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Echovirus B / mature / receptor
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 / 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 / IgG binding / beta-2-microglobulin binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / 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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / 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 / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / T=pseudo3 icosahedral viral capsid / 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 / host cell cytoplasmic vesicle membrane / 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 / viral capsid / sensory perception of smell / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / ribonucleoside triphosphate phosphatase activity / T cell differentiation in thymus / DAP12 signaling / late endosome membrane / host cell / negative regulation of neuron projection development / nucleoside-triphosphate phosphatase / protein refolding / ER-Phagosome pathway / channel activity / early endosome membrane / monoatomic ion transmembrane transport / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / DNA replication / RNA helicase activity / endosome membrane / immune response / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / Golgi membrane / external side of plasma membrane / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / lysosomal membrane / cysteine-type endopeptidase activity / focal adhesion / viral RNA genome replication / RNA-directed RNA polymerase activity / Neutrophil degranulation / DNA-templated transcription / 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 / proteolysis / :
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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 superfamily / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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) / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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 / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / Genome polyprotein / Genome polyprotein / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin / Genome polyprotein / VP4
Similarity search - Component
Biological speciesHomo sapiens (human)
Echovirus E30
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang, K. / Zhu, L. / Sun, Y. / Li, M. / Zhao, X. / Cui, L. / Zhang, L. / Gao, G. / Zhai, W. / Zhu, F. ...Wang, K. / Zhu, L. / Sun, Y. / Li, M. / Zhao, X. / Cui, L. / Zhang, L. / Gao, G. / Zhai, W. / Zhu, F. / Rao, Z. / Wang, X.
Funding support China, 1items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 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
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Revision 1.3Nov 13, 2024Group: Author supporting evidence / Data collection / Structure summary
Category: em_admin / em_entity_assembly_molwt / em_virus_natural_host
Item: _em_admin.last_update / _em_entity_assembly_molwt.entity_assembly_id ..._em_admin.last_update / _em_entity_assembly_molwt.entity_assembly_id / _em_entity_assembly_molwt.id / _em_virus_natural_host.id / _em_virus_natural_host.ncbi_tax_id / _em_virus_natural_host.organism

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,8367
Polymers136,6076
Non-polymers2281
Water00
1
A: VP1
B: VP2
C: VP3
D: VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,210,141420
Polymers8,196,439360
Non-polymers13,70260
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: VP1
B: VP2
C: VP3
D: VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 5


  • icosahedral pentamer
  • 684 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)684,17835
Polymers683,03730
Non-polymers1,1425
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 821 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)821,01442
Polymers819,64436
Non-polymers1,3706
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
6
A: VP1
B: VP2
C: VP3
D: VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 8.21 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)8,210,141420
Polymers8,196,439360
Non-polymers13,70260
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30901699, -0.809017, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.809017)236.88, -146.39989, 90.48011
3generate(-0.809017, -0.5, 0.309017), (0.5, -0.30901699, 0.809017), (-0.309017, 0.80901699, 0.5)473.76
4generate(-0.80901699, 0.5, -0.309017), (-0.5, -0.309017, 0.809017), (0.30901699, 0.809017, 0.5)383.27989, 236.88, -146.39989
5generate(0.309017, 0.80901699, -0.5), (-0.80901699, 0.5, 0.309017), (0.5, 0.309017, 0.80901699)90.48011, 236.88, -146.39989
6generate(-0.5, -0.30901699, -0.80901699), (-0.309017, -0.80901699, 0.50000001), (-0.809017, 0.49999999, 0.30901699)620.15989, 383.27989, 236.88
7generate(-1), (-1), (1)473.76, 473.76
8generate(0.5, -0.30901699, -0.80901699), (-0.30901699, 0.809017, -0.5), (0.809017, 0.5, 0.30901699)383.27989, 236.88, -146.39989
9generate(0.30901699, -0.80901699, -0.5), (0.809017, 0.5, -0.30901699), (0.5, -0.309017, 0.80901699)473.76
10generate(-0.309017, -0.80901699, -0.5), (0.80901699, -0.5, 0.309017), (-0.5, -0.309017, 0.80901699)620.15989, 90.48011, 236.88
11generate(0.30901699, 0.809017, 0.49999999), (0.80901699, -0.5, 0.30901699), (0.50000001, 0.309017, -0.80901699)-146.39989, 90.48011, 236.88
12generate(0.5, 0.309017, 0.80901699), (-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.30901699)-146.39989, 383.27989, 236.88
13generate(1), (-1), (-1)473.76, 473.76
14generate(-0.5, 0.30901699, 0.809017), (-0.30901699, 0.80901699, -0.5), (-0.809017, -0.5, -0.30901699)90.48011, 236.88, 620.15989
15generate(-0.309017, 0.80901699, 0.5), (0.80901699, 0.5, -0.309017), (-0.5, 0.309017, -0.80901699)473.76
16generate(-0.80901699, -0.50000001, 0.309017), (-0.49999999, 0.30901699, -0.809017), (0.30901699, -0.80901699, -0.5)473.76, 473.76, 473.76
17generate(-0.80901699, 0.5, -0.30901699), (0.5, 0.30901699, -0.809017), (-0.309017, -0.80901699, -0.5)383.27989, 236.88, 620.15989
18generate(0.30901699, 0.809017, -0.5), (0.80901699, -0.5, -0.309017), (-0.5, -0.30901699, -0.80901699)90.48011, 236.88, 620.15989
19generate(1), (-1), (-1)473.76, 473.76
20generate(0.309017, -0.80901699, 0.5), (-0.80901699, -0.5, -0.309017), (0.5, -0.309017, -0.80901699)236.88, 620.15989, 383.27989
21generate(-0.309017, -0.80901699, 0.50000001), (0.809017, -0.49999999, -0.30901699), (0.5, 0.30901699, 0.80901699)383.27989, 236.88, -146.39989
22generate(-1), (-1), (1)473.76, 473.76
23generate(-0.30901699, 0.809017, -0.5), (-0.809017, -0.5, -0.30901699), (-0.5, 0.30901699, 0.80901699)236.88, 620.15989, 90.48011
24generate(0.809017, 0.5, -0.30901699), (-0.5, 0.309017, -0.80901699), (-0.30901699, 0.80901699, 0.5)473.76
25generate(0.80901699, -0.5, 0.309017), (0.5, 0.309017, -0.80901699), (0.309017, 0.80901699, 0.5)90.48011, 236.88, -146.39989
26generate(1), (-1), (-1)473.76, 473.76
27generate(0.80901699, 0.5, 0.30901699), (0.5, -0.30901699, -0.809017), (-0.30901699, 0.809017, -0.5)-146.39989, 383.27989, 236.88
28generate(0.5, -0.30901699, 0.809017), (0.309017, -0.80901699, -0.5), (0.809017, 0.5, -0.309017)473.76
29generate(-0.5, -0.309017, 0.809017), (-0.30901699, -0.809017, -0.5), (0.80901699, -0.5, 0.309017)236.88, 620.15989, 90.48011
30generate(-0.80901699, 0.5, 0.309017), (-0.5, -0.309017, -0.80901699), (-0.309017, -0.80901699, 0.5)236.88, 620.15989, 383.27989
31generate(-0.49999999, 0.30901699, -0.809017), (-0.30901699, 0.80901699, 0.5), (0.80901699, 0.50000001, -0.309017)473.76
32generate(0.5, 0.30901699, -0.809017), (0.309017, 0.80901699, 0.5), (0.80901699, -0.5, 0.30901699)236.88, -146.39989, 90.48011
33generate(0.80901699, -0.5, -0.309017), (0.5, 0.30901699, 0.80901699), (-0.30901699, -0.809017, 0.5)236.88, -146.39989, 383.27989
34generate(-1), (1), (-1)473.76, 473.76
35generate(-0.80901699, -0.5, -0.309017), (-0.5, 0.309017, 0.80901699), (-0.309017, 0.80901699, -0.5)620.15989, 90.48011, 236.88
36generate(0.80901699, -0.5, 0.30901699), (-0.50000001, -0.309017, 0.80901699), (-0.30901699, -0.809017, -0.49999999)90.48011, 236.88, 620.15989
37generate(-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.30901699), (-0.5, -0.309017, -0.80901699)383.27989, 236.88, 620.15989
38generate(-1), (1), (-1)473.76, 473.76
39generate(-0.30901699, 0.80901699, -0.5), (0.809017, 0.5, 0.30901699), (0.5, -0.30901699, -0.809017)236.88, -146.39989, 383.27989
40generate(0.80901699, 0.5, -0.309017), (0.5, -0.309017, 0.80901699), (0.309017, -0.80901699, -0.5)473.76
41generate(-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.50000001, 0.309017), (0.49999999, -0.30901699, 0.809017)473.76
42generate(0.309017, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.809017)-146.39989, 383.27989, 236.88
43generate(0.5, 0.30901699, 0.80901699), (0.30901699, 0.809017, -0.5), (-0.80901699, 0.5, 0.309017)-146.39989, 90.48011, 236.88
44generate(1), (1), (1)
45generate(-0.5, 0.309017, 0.80901699), (0.309017, -0.80901699, 0.5), (0.80901699, 0.5, 0.309017)90.48011, 236.88, -146.39989
46generate(-0.50000001, -0.309017, 0.80901699), (0.30901699, 0.809017, 0.49999999), (-0.80901699, 0.5, -0.30901699)236.88, -146.39989, 383.27989
47generate(-0.809017, 0.5, 0.30901699), (0.5, 0.309017, 0.80901699), (0.309017, 0.809017, -0.5)236.88, -146.39989, 90.48011
48generate(1), (1), (1)
49generate(0.809017, 0.5, 0.30901699), (-0.5, 0.30901699, 0.809017), (0.30901699, -0.80901699, 0.5)-146.39989, 90.48011, 236.88
50generate(0.5, -0.309017, 0.80901699), (-0.309017, 0.80901699, 0.5), (-0.80901699, -0.5, 0.309017)473.76
51generate(0.809017, -0.49999999, -0.30901699), (-0.5, -0.30901699, -0.80901699), (0.309017, 0.80901699, -0.50000001)236.88, 620.15989, 90.48011
52generate(-1), (-1), (1)473.76, 473.76
53generate(-0.809017, -0.5, -0.30901699), (0.5, -0.30901699, -0.80901699), (0.30901699, -0.809017, 0.5)620.15989, 383.27989, 236.88
54generate(-0.5, 0.309017, -0.80901699), (0.30901699, -0.80901699, -0.5), (-0.809017, -0.5, 0.30901699)473.76, 473.76, 473.76
55generate(0.5, 0.309017, -0.80901699), (-0.309017, -0.80901699, -0.5), (-0.80901699, 0.5, -0.309017)236.88, 620.15989, 383.27989
56generate(-1), (1), (-1)473.76, 473.76
57generate(0.5, -0.30901699, -0.809017), (0.30901699, -0.809017, 0.5), (-0.80901699, -0.5, -0.30901699)383.27989, 236.88, 620.15989
58generate(0.309017, -0.80901699, -0.5), (-0.809017, -0.5, 0.309017), (-0.5, 0.30901699, -0.809017)473.76, 473.76, 473.76
59generate(-0.30901699, -0.809017, -0.5), (-0.80901699, 0.5, -0.309017), (0.5, 0.309017, -0.809017)620.15989, 383.27989, 236.88
60generate(-0.5, -0.309017, -0.80901699), (0.309017, 0.80901699, -0.5), (0.80901699, -0.5, -0.309017)620.15989, 90.48011, 236.88

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Components

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Protein , 6 types, 6 molecules ABCDEF

#1: Protein VP1


Mass: 33091.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: A0A0F6T703*PLUS
#2: Protein VP2


Mass: 28878.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: A0A0F6T703*PLUS
#3: Protein VP3


Mass: 26157.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: A8BJF8*PLUS
#4: Protein VP4


Mass: 7437.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: Q33C85, UniProt: Q8QWB2*PLUS
#5: Protein IgG receptor FcRn large subunit p51 / FCGRT / 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 / Production host: Homo sapiens (human) / References: UniProt: P55899
#6: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Homo sapiens (human) / References: UniProt: P61769

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1Echovirus E30COMPLEXParticles purified from the cell cultures innoculated with the live E30.#1-#60NATURAL
2E30 F-particle in complex with FcRnCOMPLEX#1-#41NATURAL
3E30 F-particle in complex with FcRnCOMPLEX#5-#61RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Echovirus E3041846
31Echovirus E3041846
41human (human)41846
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural host
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens9606
22Homo sapiens9606
33Homo sapiens9606
Virus shellDiameter: 30 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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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: DARK FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 25

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2RELION3image acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7299 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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