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- PDB-7c9s: Echovirus 30 F-particle -

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Basic information

Entry
Database: PDB / ID: 7c9s
TitleEchovirus 30 F-particle
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Echovirus B / mature
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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / 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 / structural molecule activity / virion attachment to host cell / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SPHINGOSINE / Genome polyprotein / Genome polyprotein / Genome polyprotein / VP4
Similarity search - Component
Biological speciesEchovirus E30
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang, K. / Sun, Y. / Zhu, L. / Li, M. / Zhao, X. / Cui, L. / Zhang, L. / Gao, G. / Zhai, W. / Zhu, F. ...Wang, K. / Sun, Y. / Zhu, L. / 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

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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-30315
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  • Superimposition on EM map
  • EMDB-30315
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0745
Polymers95,7754
Non-polymers2991
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,764,442300
Polymers5,746,472240
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
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 480 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)480,37025
Polymers478,87320
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 576 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)576,44430
Polymers574,64724
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
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 5.76 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)5,764,442300
Polymers5,746,472240
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, -3.0E-8), (0.95105652, 0.309017, 4.0E-8), (-3.0E-8, -4.0E-8, 1)398.1289, -63.05744, 2.0E-5
3generate(-0.809017, -0.58778525, -8.0E-8), (0.58778526, -0.80901699, 2.0E-8), (-8.0E-8, -2.0E-8, 1)581.12869, 296.09983, 2.0E-5
4generate(-0.80901699, 0.58778525, -7.0E-8), (-0.58778526, -0.809017, -3.0E-8), (-7.0E-8, 3.0E-8, 1)296.09987, 581.12867, 1.0E-5
5generate(0.309017, 0.95105651, -3.0E-8), (-0.95105652, 0.30901699, -4.0E-8), (-3.0E-8, 4.0E-8, 1)-63.05741, 398.12891
6generate(-0.94721357, -0.16245988, -0.27639326), (-0.16245988, -0.5, 0.8506508), (-0.27639325, 0.8506508, 0.44721357)578.52573, 196.83122, -5.20588
7generate(-0.44721361, 0.85065078, -0.27639323), (-0.52573115, 0.85065079), (0.72360677, 0.52573114, 0.44721361)211.65693, 163.67998, -168.88588
8generate(0.67082038, 0.68819098, -0.27639319), (-0.16245989, 0.5, 0.85065081), (0.72360681, -0.52573109, 0.44721361)-20.0316, -45.62878, 86.05164
9generate(0.86180342, -0.42532537, -0.27639318), (0.42532537, 0.309017, 0.85065083), (-0.27639319, -0.85065082, 0.44721357)203.64582, -141.83746, 407.29169
10generate(-0.13819656, -0.95105651, -0.27639322), (0.42532537, -0.30901699, 0.85065083), (-0.89442722, -3.0E-8, 0.44721355)573.57459, 8.01106, 350.89144
11generate(-0.86180343, -0.42532536, 0.27639318), (-0.42532537, 0.309017, -0.85065083), (0.27639318, -0.85065083, -0.44721357)487.52295, 476.90892, 490.12591
12generate(-0.67082037, 0.68819098, 0.27639319), (0.16245989, 0.49999999, -0.8506508), (-0.72360681, -0.52573108, -0.44721361)171.23403, 288.08877, 653.80588
13generate(0.44721362, 0.85065078, 0.27639324), (0.52573115, -0.85065079), (-0.72360676, 0.52573115, -0.44721361)-139.2345, 321.24002, 398.86834
14generate(0.94721357, -0.16245989, 0.27639326), (0.16245987, -0.5, -0.85065081), (0.27639327, 0.8506508, -0.44721357)-14.82569, 530.54877, 77.62831
15generate(0.13819655, -0.95105651, 0.27639322), (-0.42532538, -0.30901699, -0.85065083), (0.89442722, -4.0E-8, -0.44721355)372.53172, 626.75744, 134.02859
16generate(0.809017, 0.58778524, 8.0E-8), (0.58778525, -0.809017, 2.0E-8), (7.0E-8, 2.0E-8, -1)-96.20869, 296.09984, 484.91998
17generate(0.80901699, -0.58778525, 7.0E-8), (-0.58778527, -0.80901699, -2.0E-8), (8.0E-8, -2.0E-8, -1)188.82013, 581.12867, 484.91999
18generate(-0.309017, -0.95105651, 3.0E-8), (-0.95105652, 0.309017, -4.0E-8), (3.0E-8, -4.0E-8, -1)547.97741, 398.1289, 484.92001
19generate(-1), (1.0E-8, 1), (-1)484.92, 484.92001
20generate(-0.30901699, 0.95105651, 3.0E-8), (0.95105653, 0.30901699, 4.0E-8), (3.0E-8, 4.0E-8, -1)86.79109, -63.05744, 484.91999
21generate(-0.13819655, -0.42532537, -0.89442721), (0.95105652, -0.30901699, 4.0E-8), (-0.27639324, -0.85065082, 0.44721355)595.95435, 86.79108, 407.2917
22generate(-0.44721352, -0.89442722), (-1), (-0.89442723, 0.44721352)567.75422, 484.91999, 350.89143
23generate(-0.13819655, 0.42532536, -0.89442721), (-0.95105652, -0.309017, -4.0E-8), (-0.27639322, 0.85065083, 0.44721355)389.70557, 547.97743, -5.20589
24generate(0.36180341, 0.26286553, -0.89442719), (-0.58778525, 0.80901699, -2.0E-8), (0.7236068, 0.52573112, 0.44721359)307.86559, 188.82016, -168.88587
25generate(0.36180341, -0.26286553, -0.89442719), (0.58778526, 0.809017, 3.0E-8), (0.72360679, -0.52573112, 0.44721359)435.33434, -96.20868, 86.05166
26generate(0.44721361, -0.52573115, -0.72360676), (-0.8506508, -0.52573114), (0.27639325, 0.85065078, -0.44721361)436.94306, 576.17756, 77.62833
27generate(-0.36180341, -0.58778525, -0.72360679), (-0.26286553, 0.809017, -0.52573112), (0.8944272, -3.0E-8, -0.44721359)648.14297, 237.50888, 134.0286
28generate(-0.67082037, 0.16245988, -0.7236068), (0.68819099, 0.5, -0.52573108), (0.27639319, -0.8506508, -0.44721361)541.16279, 81.83997, 490.12591
29generate(-0.05278634, 0.68819097, -0.72360678), (0.68819098, -0.50000001, -0.52573108), (-0.72360679, -0.52573108, -0.44721365)263.8455, 324.29997, 653.80588
30generate(0.63819666, 0.26286553, -0.72360675), (-0.26286554, -0.809017, -0.52573112), (-0.72360675, 0.52573112, -0.44721365)199.43416, 629.8174, 398.86835
31generate(0.05278635, 0.68819098, 0.72360678), (-0.68819099, -0.5, 0.52573108), (0.72360678, -0.52573108, 0.44721365)-112.64306, 403.08002, 86.05163
32generate(0.67082037, 0.16245988, 0.72360681), (-0.68819099, 0.5, 0.52573108), (-0.2763932, -0.8506508, 0.44721361)-135.02284, 160.62002, 407.29167
33generate(0.3618034, -0.58778525, 0.72360679), (0.26286554, 0.809017, 0.52573112), (-0.8944272, -2.0E-8, 0.44721359)121.80585, -144.89741, 350.89142
34generate(-0.44721361, -0.52573114, 0.72360676), (0.8506508, 0.52573114), (-0.27639324, 0.85065079, 0.44721361)302.91448, -91.25757, -5.20589
35generate(-0.63819666, 0.26286553, 0.72360675), (0.26286553, -0.809017, 0.52573112), (0.72360676, 0.52573112, 0.44721365)158.01709, 247.41111, -168.88588
36generate(-0.3618034, 0.26286554, 0.89442719), (0.58778526, 0.80901699, 2.0E-8), (-0.7236068, 0.52573112, -0.44721359)49.58566, -96.20868, 398.86835
37generate(0.13819656, 0.42532537, 0.89442721), (0.95105652, -0.309017, 3.0E-8), (0.27639323, 0.85065082, -0.44721355)-111.03435, 86.79108, 77.6283
38generate(0.44721352, 0.89442722), (-1.0E-8, -1), (0.89442723, -0.44721352)-82.83422, 484.91999, 134.02857
39generate(0.13819655, -0.42532537, 0.89442721), (-0.95105653, -0.30901699, -4.0E-8), (0.27639322, -0.85065083, -0.44721355)95.21443, 547.97743, 490.12589
40generate(-0.36180341, -0.26286553, 0.89442719), (-0.58778525, 0.809017, -3.0E-8), (-0.7236068, -0.52573112, -0.44721359)177.05441, 188.82015, 653.80588
41generate(-0.13819655, 0.95105651, -0.27639323), (-0.42532537, -0.309017, -0.85065083), (-0.89442722, 4.0E-8, 0.44721355)112.38828, 626.75745, 350.89142
42generate(0.86180342, 0.42532536, -0.27639319), (-0.42532538, 0.30901699, -0.85065083), (-0.27639318, 0.85065083, 0.44721358)-2.60295, 476.90893, -5.20591
43generate(0.67082037, -0.68819098, -0.2763932), (0.16245988, 0.5, -0.8506508), (0.72360681, 0.52573108, 0.44721362)313.68597, 288.08877, -168.88587
44generate(-0.44721362, -0.85065078, -0.27639324), (0.52573115, -0.85065079), (0.72360676, -0.52573115, 0.44721362)624.1545, 321.24001, 86.05166
45generate(-0.94721357, 0.16245988, -0.27639326), (0.16245989, -0.5, -0.8506508), (-0.27639327, -0.8506508, 0.44721357)499.74569, 530.54876, 407.2917
46generate(0.05278634, -0.68819098, 0.72360678), (0.68819098, -0.5, -0.52573109), (0.72360679, 0.52573108, 0.44721366)221.0745, 324.29997, -168.88588
47generate(-0.63819666, -0.26286553, 0.72360675), (-0.26286554, -0.80901699, -0.52573113), (0.72360675, -0.52573112, 0.44721366)285.48584, 629.8174, 86.05165
48generate(-0.44721361, 0.52573115, 0.72360676), (-0.85065079, -0.52573115), (-0.27639324, -0.85065078, 0.44721361)47.97694, 576.17756, 407.29168
49generate(0.36180341, 0.58778525, 0.72360679), (-0.26286553, 0.80901699, -0.52573113), (-0.8944272, 3.0E-8, 0.44721359)-163.22297, 237.50889, 350.89141
50generate(0.67082038, -0.16245988, 0.7236068), (0.68819099, 0.5, -0.52573109), (-0.27639319, 0.8506508, 0.44721362)-56.24279, 81.83997, -5.20591
51generate(-0.3618034, 0.58778525, -0.72360679), (0.26286554, 0.80901699, 0.52573113), (0.8944272, 2.0E-8, -0.44721359)363.11415, -144.89741, 134.02859
52generate(0.44721362, 0.52573114, -0.72360675), (0.85065079, 0.52573115), (0.27639323, -0.85065079, -0.44721362)182.00551, -91.25757, 490.1259
53generate(0.63819666, -0.26286554, -0.72360675), (0.26286553, -0.80901699, 0.52573113), (-0.72360676, -0.52573112, -0.44721366)326.90291, 247.4111, 653.80589
54generate(-0.05278635, -0.68819098, -0.72360678), (-0.68819099, -0.49999999, 0.52573109), (-0.72360678, 0.52573109, -0.44721366)597.56306, 403.08001, 398.86837
55generate(-0.67082038, -0.16245988, -0.7236068), (-0.68819098, 0.5, 0.52573109), (0.2763932, 0.8506508, -0.44721361)619.94284, 160.62002, 77.62833
56generate(0.44721361, -0.85065078, 0.27639324), (-0.52573115, 0.85065079), (-0.72360677, -0.52573114, -0.44721362)273.26307, 163.67997, 653.80588
57generate(-0.67082038, -0.68819097, 0.27639319), (-0.16245988, 0.50000001, 0.8506508), (-0.72360681, 0.52573108, -0.44721362)504.95159, -45.62878, 398.86837
58generate(-0.86180342, 0.42532537, 0.27639319), (0.42532538, 0.30901699, 0.85065083), (0.27639319, 0.85065082, -0.44721357)281.27417, -141.83746, 77.62832
59generate(0.13819656, 0.95105651, 0.27639323), (0.42532537, -0.309017, 0.85065083), (0.89442722, 4.0E-8, -0.44721355)-88.6546, 8.01106, 134.02857
60generate(0.94721357, 0.16245988, 0.27639326), (-0.16245989, -0.5, 0.8506508), (0.27639326, -0.8506508, -0.44721358)-93.60574, 196.83122, 490.12589

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Components

#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: 7647.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: Q33C85, UniProt: Q8QWB2*PLUS
#5: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Feature type: SUBJECT OF INVESTIGATION
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

ComponentName: Echovirus E30 / Type: VIRUS
Details: Particles purified from the cell cultures innoculated with the live E30.
Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Echovirus E30
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
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 / 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)
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
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19272 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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