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- PDB-7c80: E30 F-particle in complex with 4B10 -

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Basic information

Entry
Database: PDB / ID: 7c80
TitleE30 F-particle in complex with 4B10
Components
  • Heavy chain
  • Light chain
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS/IMMUNE SYSTEM / MAb / 4B10 / E30 F-particle / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SPHINGOSINE / Genome polyprotein / Genome polyprotein / Genome polyprotein / VP4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Echovirus E30
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, K. / Zheng, B. / Zhang, L. / Cui, L. / Su, X. / Zhang, Q. / Guo, Y. / Zhu, L. / 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: Serotype specific epitopes identified by neutralizing antibodies underpin immunogenic differences in Enterovirus B.
Authors: Kang Wang / Binyang Zheng / Li Zhang / Lunbiao Cui / Xuan Su / Qian Zhang / Zhenxi Guo / Yu Guo / Wei Zhang / Ling Zhu / Fengcai Zhu / Zihe Rao / Xiangxi Wang /
Abstract: Echovirus 30 (E30), a serotype of Enterovirus B (EV-B), recently emerged as a major causative agent of aseptic meningitis worldwide. E30 is particularly devastating in the neonatal population and ...Echovirus 30 (E30), a serotype of Enterovirus B (EV-B), recently emerged as a major causative agent of aseptic meningitis worldwide. E30 is particularly devastating in the neonatal population and currently no vaccine or antiviral therapy is available. Here we characterize two highly potent E30-specific monoclonal antibodies, 6C5 and 4B10, which efficiently block binding of the virus to its attachment receptor CD55 and uncoating receptor FcRn. Combinations of 6C5 and 4B10 augment the sum of their individual anti-viral activities. High-resolution structures of E30-6C5-Fab and E30-4B10-Fab define the location and nature of epitopes targeted by the antibodies. 6C5 and 4B10 engage the capsid loci at the north rim of the canyon and in-canyon, respectively. Notably, these regions exhibit antigenic variability across EV-Bs, highlighting challenges in development of broad-spectrum antibodies. Our structures of these neutralizing antibodies of E30 are instructive for development of vaccines and therapeutics against EV-B infections.
History
DepositionMay 28, 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.title / _citation.year

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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
  • EMDB-30303
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  • Superimposition on EM map
  • EMDB-30303
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Light chain
H: Heavy chain
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,1307
Polymers141,8316
Non-polymers2991
Water0
1
L: Light chain
H: Heavy chain
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,527,805420
Polymers8,509,836360
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
L: Light chain
H: Heavy chain
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 711 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)710,65035
Polymers709,15330
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
L: Light chain
H: Heavy chain
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 853 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)852,78142
Polymers850,98436
Non-polymers1,7976
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
L: Light chain
H: Heavy chain
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 8.53 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)8,527,805420
Polymers8,509,836360
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30901699, -0.95105651, -4.8E-7), (0.95105652, 0.309017, 6.6E-7), (-4.8E-7, -6.6E-7, 1)495.87966, -78.53979, 0.00034
3generate(-0.809017, -0.58778525, -1.25E-6), (0.58778526, -0.80901699, 4.1E-7), (-1.25E-6, -4.0E-7, 1)723.81068, 368.79966, 0.0005
4generate(-0.80901699, 0.58778525, -1.26E-6), (-0.58778526, -0.809017, -4.1E-7), (-1.25E-6, 4.1E-7, 1)368.80014, 723.81044, 0.00025
5generate(0.309017, 0.95105651, -4.8E-7), (-0.95105652, 0.30901699, -6.6E-7), (-4.8E-7, 6.6E-7, 1)-78.53946, 495.87971, -6.0E-5
6generate(-0.94721398, 0.16245926, 0.27639223), (0.16245926, -0.5, 0.85065093), (0.27639224, 0.85065092, 0.44721398)455.51038, 147.03586, -173.41992
7generate(-0.13819741, 0.95105651, 0.27639279), (-0.425326, -0.30901699, 0.85065052), (0.89442679, 6.6E-7, 0.44721441)-26.95319, 266.86629, -103.17242
8generate(0.86180302, 0.42532599, 0.27639349), (-0.425326, 0.30901699, 0.85065052), (0.27639349, -0.85065051, 0.44721398)-170.17816, 80.22621, 340.35573
9generate(0.6708207, -0.68819059, 0.27639335), (0.16245926, 0.5, 0.85065092), (-0.72360665, -0.52573159, 0.44721328)223.7675, -154.95414, 544.22371
10generate(-0.44721329, -0.85065117, 0.27639258), (0.52573053, 0.85065118), (-0.72360742, 0.52573052, 0.44721328)610.46429, -113.6635, 226.6929
11generate(-0.86180302, 0.42532599, -0.27639349), (0.425326, 0.30901699, -0.85065052), (-0.27639349, -0.85065051, -0.44721398)517.26975, 337.11371, 777.40016
12generate(0.13819741, 0.95105651, -0.27639279), (0.425326, -0.30901699, -0.85065052), (-0.89442679, 6.5E-7, -0.44721441)56.51406, 523.7538, 707.15201
13generate(0.94721398, 0.16245926, -0.27639223), (-0.16245926, -0.5, -0.85065092), (-0.27639224, 0.85065092, -0.44721398)50.34747, 758.93415, 263.62376
14generate(0.44721329, -0.85065117, -0.27639258), (-0.52573053, -0.85065118), (0.72360742, 0.52573052, -0.44721328)507.292, 717.64351, 59.75637
15generate(-0.6708207, -0.68819059, -0.27639335), (-0.16245926, 0.5, -0.85065093), (0.72360665, -0.52573159, -0.44721328)795.86584, 456.94414, 377.28765
16generate(0.809017, -0.58778524, 1.26E-6), (-0.58778526, -0.809017, -4.1E-7), (1.25E-6, -4.1E-7, -1)235.17984, 723.81044, 603.97974
17generate(-0.30901699, -0.95105651, 4.8E-7), (-0.95105652, 0.30901699, -6.6E-7), (4.8E-7, -6.6E-7, -1)682.51945, 495.87971, 603.98005
18generate(-1), (1), (-1)603.97999, 603.97999
19generate(-0.309017, 0.95105651, 4.8E-7), (0.95105652, 0.309017, 6.6E-7), (4.8E-7, 6.5E-7, -1)108.10033, -78.53979, 603.97965
20generate(0.80901699, 0.58778525, 1.25E-6), (0.58778526, -0.80901699, 4.1E-7), (1.25E-6, 4.1E-7, -1)-119.83069, 368.79966, 603.97949
21generate(0.05278741, -0.68819059, -0.72360707), (0.6881906, -0.5, 0.52573159), (-0.72360707, -0.52573159, 0.44721259)712.3975, 86.39265, 544.22405
22generate(-0.6381956, -0.26286592, -0.72360755), (-0.26286592, -0.80901699, 0.52573093), (-0.72360755, 0.52573093, 0.44721259)792.6238, 466.92244, 226.69302
23generate(-0.44721328, 0.52573051, -0.72360742), (-0.85065118, 0.52573052), (0.27639259, 0.85065117, 0.44721328)496.80077, 400.11279, -173.41989
24generate(0.36180328, 0.58778524, -0.72360686), (-0.26286592, 0.809017, 0.52573093), (0.89442714, 4.1E-7, 0.44721371)233.74579, -21.70765, -103.17224
25generate(0.6708207, -0.16245926, -0.72360664), (0.6881906, 0.5, 0.52573159), (0.27639336, -0.85065092, 0.44721329)366.99189, -215.59736, 340.3561
26generate(-0.36180328, -0.26286592, -0.89442713), (-0.58778526, 0.80901699, -4.1E-7), (0.72360686, 0.52573093, -0.44721371)760.74189, 235.18035, 59.75655
27generate(-0.36180328, 0.26286591, -0.89442713), (0.58778526, 0.809017, 4.1E-7), (0.72360686, -0.52573093, -0.44721371)601.97613, -119.83043, 377.28752
28generate(0.13819741, 0.42532599, -0.89442678), (0.95105652, -0.30901699, 6.6E-7), (-0.2763928, -0.85065051, -0.44721441)401.9195, 108.10029, 777.40008
29generate(0.44721483, -0.89442657), (-1), (-0.89442658, -0.44721483)437.04346, 603.98001, 707.15228
30generate(0.13819741, -0.42532599, -0.89442678), (-0.95105652, -0.309017, -6.6E-7), (-0.2763928, 0.85065051, -0.44721441)658.80789, 682.5198, 263.62418
31generate(-0.13819741, 0.42532599, 0.89442678), (-0.95105652, -0.309017, -6.6E-7), (0.2763928, -0.85065051, 0.44721441)-54.82791, 682.5198, 340.35581
32generate(0.36180328, 0.26286592, 0.89442713), (-0.58778526, 0.80901699, -4.1E-7), (-0.72360686, -0.52573093, 0.44721371)-156.7619, 235.18035, 544.22344
33generate(0.36180328, -0.26286592, 0.89442713), (0.58778526, 0.809017, 4.1E-7), (-0.72360686, 0.52573093, 0.44721371)2.00386, -119.83043, 226.69248
34generate(-0.13819741, -0.42532599, 0.89442678), (0.95105652, -0.30901699, 6.6E-7), (0.2763928, 0.85065051, 0.44721441)202.06049, 108.10029, -173.42009
35generate(-0.44721483, 0.89442657), (-1), (0.89442658, 0.44721483)166.93652, 603.98001, -103.17229
36generate(0.44721328, 0.52573052, 0.72360742), (0.85065118, -0.52573052), (-0.27639259, 0.85065117, -0.44721329)-210.3515, 203.86722, 263.62358
37generate(0.6381956, -0.26286591, 0.72360755), (0.26286592, -0.80901699, -0.52573093), (0.72360755, 0.52573093, -0.44721259)-29.87805, 625.68765, 59.756
38generate(-0.0527874, -0.68819059, 0.72360707), (-0.6881906, -0.5, -0.52573159), (0.72360708, -0.52573158, -0.44721259)307.23584, 819.57736, 377.28731
39generate(-0.6708207, -0.16245926, 0.72360664), (-0.6881906, 0.5, -0.52573159), (-0.27639336, -0.85065092, -0.44721328)335.11024, 517.58736, 777.40004
40generate(-0.36180328, 0.58778525, 0.72360685), (0.26286592, 0.80901699, -0.52573093), (-0.89442714, 4.0E-7, -0.44721371)15.22367, 137.05756, 707.15199
41generate(0.05278741, 0.68819059, -0.72360707), (-0.6881906, -0.5, -0.52573159), (-0.72360707, 0.52573159, 0.44721259)296.74414, 819.57736, 226.69268
42generate(0.6708207, 0.16245926, -0.72360664), (-0.6881906, 0.5, -0.52573159), (0.27639336, 0.85065092, 0.44721329)268.86975, 517.58736, -173.42005
43generate(0.36180328, -0.58778525, -0.72360685), (0.26286592, 0.80901699, -0.52573093), (0.89442714, -4.0E-7, 0.44721372)588.75632, 137.05756, -103.172
44generate(-0.44721329, -0.52573052, -0.72360741), (0.85065118, -0.52573052), (0.27639258, -0.85065117, 0.44721329)814.33149, 203.86722, 340.35641
45generate(-0.6381956, 0.26286592, -0.72360755), (0.26286592, -0.809017, -0.52573093), (-0.72360755, -0.52573093, 0.44721259)633.85804, 625.68765, 544.22399
46generate(-0.13819741, -0.95105651, 0.2763928), (0.425326, -0.309017, -0.85065052), (0.89442679, -6.5E-7, 0.44721441)547.46593, 523.7538, -103.17203
47generate(-0.94721398, -0.16245926, 0.27639224), (-0.16245926, -0.5, -0.85065092), (0.27639224, -0.85065091, 0.44721398)553.63252, 758.93415, 340.35623
48generate(-0.44721328, 0.85065117, 0.27639258), (-0.52573053, -0.85065118), (-0.72360742, -0.52573052, 0.44721329)96.68799, 717.64351, 544.22362
49generate(0.6708207, 0.68819059, 0.27639336), (-0.16245926, 0.5, -0.85065092), (-0.72360665, 0.52573158, 0.44721329)-191.88585, 456.94414, 226.69234
50generate(0.86180302, -0.42532599, 0.27639349), (0.425326, 0.30901699, -0.85065052), (0.27639349, 0.85065051, 0.44721398)86.71023, 337.11371, -173.42017
51generate(0.44721328, 0.85065117, -0.27639258), (0.52573053, 0.85065118), (0.72360742, -0.52573052, -0.44721329)-6.4843, -113.6635, 377.2871
52generate(0.94721398, -0.16245925, -0.27639224), (0.16245926, -0.5, 0.85065092), (-0.27639224, -0.85065092, -0.44721398)148.46961, 147.03586, 777.39991
53generate(0.13819741, -0.95105651, -0.2763928), (-0.425326, -0.30901699, 0.85065052), (-0.89442679, -6.6E-7, -0.44721441)630.93317, 266.8663, 707.15241
54generate(-0.86180301, -0.42532599, -0.27639349), (-0.425326, 0.309017, 0.85065052), (-0.27639349, 0.85065051, -0.44721398)774.15815, 80.22621, 263.62426
55generate(-0.67082071, 0.68819059, -0.27639336), (0.16245926, 0.5, 0.85065092), (0.72360665, 0.52573159, -0.44721329)380.21249, -154.95414, 59.75628
56generate(-0.36180328, -0.58778525, 0.72360685), (-0.26286592, 0.80901699, 0.52573093), (-0.89442714, -4.1E-7, -0.44721372)370.2342, -21.70764, 707.15223
57generate(-0.6708207, 0.16245925, 0.72360664), (0.6881906, 0.5, 0.52573159), (-0.27639336, 0.85065091, -0.44721329)236.9881, -215.59736, 263.62389
58generate(-0.05278741, 0.68819059, 0.72360707), (0.6881906, -0.5, 0.52573159), (0.72360707, 0.52573159, -0.44721259)-108.41751, 86.39265, 59.75595
59generate(0.6381956, 0.26286592, 0.72360755), (-0.26286592, -0.80901699, 0.52573093), (0.72360755, -0.52573093, -0.44721259)-188.64381, 466.92244, 377.28697
60generate(0.44721329, -0.52573051, 0.72360741), (-0.85065118, 0.52573052), (-0.27639258, -0.85065117, -0.44721329)107.17922, 400.11279, 777.39988

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Components

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Protein , 6 types, 6 molecules LHABCD

#1: Protein Light chain /


Mass: 24326.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Protein Heavy chain


Mass: 21729.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: 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
#4: 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
#5: 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
#6: Protein VP4


Mass: 7647.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: Q33C85, UniProt: Q8QWB2*PLUS

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2

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Details

Has ligand of interestN

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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
IDNameTypeEntity IDParent-IDSource
1E30 F-particle in complex with 4B10COMPLEX#1-#60MULTIPLE SOURCES
2E30 F-particle in complex with 4B10COMPLEX#1-#21NATURAL
3E30 F-particle in complex with 4B10COMPLEX#3-#61NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Mus musculus (house mouse)10090
33Echovirus E3041846
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NONOSEROTYPEVIRION
22
33
Buffer solutionpH: 7.4
Buffer componentName: PBS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / 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: 2.5 nm / Nominal defocus min: 1.2 nm / Cs: 2.7 mm
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) / Num. of real images: 998
Image scansMovie frames/image: 25

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2RELION3image acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 18328
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1841 / Symmetry type: POINT

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