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- PDB-7c9t: Echovirus 30 A-particle -

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Basic information

Entry
Database: PDB / ID: 7c9t
TitleEchovirus 30 A-particle
Components
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / Echovirus B / altered particle
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 / nucleoside-triphosphate phosphatase ...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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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) / 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 / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus E30
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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-30316
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3


Theoretical massNumber of molelcules
Total (without water)88,1273
Polymers88,1273
Non-polymers00
Water00
1
A: VP1
B: VP2
C: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,287,622180
Polymers5,287,622180
Non-polymers00
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
x 5


  • icosahedral pentamer
  • 441 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)440,63515
Polymers440,63515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
x 6


  • icosahedral 23 hexamer
  • 529 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)528,76218
Polymers528,76218
Non-polymers00
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
x 60


  • crystal asymmetric unit, crystal frame
  • 5.29 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)5,287,622180
Polymers5,287,622180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.309017, -0.95105651, -2.0E-8), (0.95105653, 0.30901699, 3.0E-8), (-3.0E-8, -3.0E-8, 1)398.1289, -63.05743, 1.0E-5
3generate(-0.80901699, -0.58778525, -6.0E-8), (0.58778526, -0.809017, 2.0E-8), (-7.0E-8, -2.0E-8, 1)581.12868, 296.09984, 2.0E-5
4generate(-0.809017, 0.58778525, -6.0E-8), (-0.58778526, -0.80901699, -2.0E-8), (-6.0E-8, 3.0E-8, 1)296.09987, 581.12867
5generate(0.30901699, 0.95105651, -2.0E-8), (-0.95105653, 0.309017, -3.0E-8), (-2.0E-8, 4.0E-8, 1)-63.05741, 398.12891
6generate(-0.94721358, -0.16245987, -0.27639324), (-0.16245988, -0.5, 0.85065081), (-0.27639326, 0.8506508, 0.44721357)578.52573, 196.83122, -5.20589
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, 0.68819097, -0.27639319), (-0.16245988, 0.5, 0.8506508), (0.72360681, -0.52573109, 0.44721361)-20.0316, -45.62878, 86.05164
9generate(0.86180342, -0.42532538, -0.27639318), (0.42532538, 0.30901699, 0.85065082), (-0.27639319, -0.85065082, 0.44721358)203.64582, -141.83745, 407.29169
10generate(-0.13819656, -0.95105651, -0.27639322), (0.42532538, -0.309017, 0.85065082), (-0.89442722, -3.0E-8, 0.44721356)573.5746, 8.01107, 350.89143
11generate(-0.86180342, -0.42532537, 0.27639318), (-0.42532538, 0.30901699, -0.85065082), (0.27639319, -0.85065082, -0.44721357)487.52295, 476.90893, 490.12591
12generate(-0.67082038, 0.68819097, 0.27639319), (0.16245988, 0.5, -0.85065081), (-0.72360681, -0.52573109, -0.44721361)171.23404, 288.08877, 653.80588
13generate(0.44721361, 0.85065078, 0.27639323), (0.52573115, -0.85065079), (-0.72360677, 0.52573114, -0.44721361)-139.2345, 321.24002, 398.86834
14generate(0.94721358, -0.16245988, 0.27639324), (0.16245988, -0.5, -0.8506508), (0.27639325, 0.8506508, -0.44721358)-14.82569, 530.54877, 77.62831
15generate(0.13819656, -0.95105651, 0.27639322), (-0.42532538, -0.309017, -0.85065082), (0.89442722, -4.0E-8, -0.44721356)372.53172, 626.75745, 134.02859
16generate(0.809017, 0.58778524, 6.0E-8), (0.58778526, -0.809017, 2.0E-8), (6.0E-8, 2.0E-8, -1)-96.20868, 296.09984, 484.91998
17generate(0.80901699, -0.58778525, 6.0E-8), (-0.58778525, -0.80901699, -2.0E-8), (7.0E-8, -2.0E-8, -1)188.82014, 581.12867, 484.91999
18generate(-0.309017, -0.95105651, 2.0E-8), (-0.95105653, 0.309017, -3.0E-8), (3.0E-8, -4.0E-8, -1)547.97741, 398.12891, 484.92001
19generate(-1), (1), (-1)484.92, 484.92
20generate(-0.30901699, 0.95105651, 2.0E-8), (0.95105652, 0.30901699, 3.0E-8), (2.0E-8, 3.0E-8, -1)86.7911, -63.05743, 484.91999
21generate(-0.13819656, -0.42532538, -0.8944272), (0.95105653, -0.309017, 3.0E-8), (-0.27639323, -0.85065082, 0.44721356)595.95435, 86.79108, 407.2917
22generate(-0.44721354, -0.89442721), (-1), (-0.89442723, 0.44721354)567.75422, 484.91999, 350.89143
23generate(-0.13819656, 0.42532537, -0.8944272), (-0.95105653, -0.30901699, -3.0E-8), (-0.27639322, 0.85065082, 0.44721355)389.70557, 547.97743, -5.20589
24generate(0.36180341, 0.26286554, -0.89442719), (-0.58778526, 0.809017, -2.0E-8), (0.7236068, 0.52573112, 0.44721359)307.86559, 188.82016, -168.88588
25generate(0.36180341, -0.26286554, -0.89442719), (0.58778526, 0.80901699, 2.0E-8), (0.7236068, -0.52573112, 0.44721359)435.33434, -96.20868, 86.05166
26generate(0.44721361, -0.52573114, -0.72360676), (-0.8506508, -0.52573114), (0.27639324, 0.85065079, -0.44721361)436.94306, 576.17756, 77.62832
27generate(-0.3618034, -0.58778524, -0.72360679), (-0.26286554, 0.80901699, -0.52573112), (0.8944272, -3.0E-8, -0.44721359)648.14297, 237.50889, 134.0286
28generate(-0.67082037, 0.16245988, -0.7236068), (0.68819098, 0.5, -0.52573109), (0.2763932, -0.8506508, -0.44721361)541.16279, 81.83997, 490.12591
29generate(-0.05278635, 0.68819097, -0.72360678), (0.68819099, -0.5, -0.52573109), (-0.72360679, -0.52573108, -0.44721364)263.8455, 324.29997, 653.80588
30generate(0.63819665, 0.26286553, -0.72360676), (-0.26286554, -0.80901699, -0.52573112), (-0.72360676, 0.52573112, -0.44721364)199.43416, 629.8174, 398.86835
31generate(0.05278635, 0.68819097, 0.72360678), (-0.68819098, -0.5, 0.52573109), (0.72360679, -0.52573109, 0.44721364)-112.64306, 403.08002, 86.05164
32generate(0.67082037, 0.16245987, 0.7236068), (-0.68819099, 0.5, 0.52573109), (-0.27639319, -0.8506508, 0.44721361)-135.02283, 160.62002, 407.29167
33generate(0.3618034, -0.58778524, 0.72360679), (0.26286554, 0.80901699, 0.52573112), (-0.8944272, -2.0E-8, 0.44721359)121.80585, -144.89741, 350.89142
34generate(-0.44721361, -0.52573113, 0.72360677), (0.8506508, 0.52573114), (-0.27639324, 0.85065079, 0.44721361)302.91448, -91.25757, -5.20589
35generate(-0.63819665, 0.26286554, 0.72360676), (0.26286554, -0.80901699, 0.52573112), (0.72360676, 0.52573112, 0.44721364)158.01709, 247.41111, -168.88588
36generate(-0.36180341, 0.26286554, 0.89442719), (0.58778525, 0.80901699, 2.0E-8), (-0.7236068, 0.52573112, -0.44721359)49.58566, -96.20868, 398.86835
37generate(0.13819656, 0.42532537, 0.8944272), (0.95105653, -0.309017, 3.0E-8), (0.27639322, 0.85065082, -0.44721356)-111.03435, 86.79108, 77.6283
38generate(0.44721354, 0.89442721), (-1), (0.89442723, -0.44721354)-82.83422, 484.91999, 134.02857
39generate(0.13819656, -0.42532537, 0.8944272), (-0.95105652, -0.30901699, -3.0E-8), (0.27639323, -0.85065082, -0.44721355)95.21443, 547.97743, 490.12589
40generate(-0.36180341, -0.26286553, 0.89442719), (-0.58778526, 0.80901699, -2.0E-8), (-0.7236068, -0.52573112, -0.44721359)177.05441, 188.82016, 653.80588
41generate(-0.13819657, 0.95105651, -0.27639322), (-0.42532538, -0.30901699, -0.85065082), (-0.89442722, 4.0E-8, 0.44721356)112.38828, 626.75745, 350.89142
42generate(0.86180342, 0.42532537, -0.27639319), (-0.42532538, 0.309017, -0.85065082), (-0.27639319, 0.85065082, 0.44721358)-2.60295, 476.90893, -5.20591
43generate(0.67082038, -0.68819097, -0.27639319), (0.16245988, 0.5, -0.85065081), (0.72360681, 0.52573108, 0.44721361)313.68597, 288.08877, -168.88588
44generate(-0.44721361, -0.85065078, -0.27639323), (0.52573115, -0.85065079), (0.72360677, -0.52573114, 0.44721361)624.1545, 321.24002, 86.05166
45generate(-0.94721358, 0.16245987, -0.27639325), (0.16245988, -0.5, -0.8506508), (-0.27639325, -0.8506508, 0.44721358)499.74569, 530.54877, 407.29169
46generate(0.05278636, -0.68819097, 0.72360678), (0.68819099, -0.5, -0.52573109), (0.72360679, 0.52573109, 0.44721364)221.0745, 324.29997, -168.88588
47generate(-0.63819665, -0.26286554, 0.72360676), (-0.26286554, -0.809017, -0.52573112), (0.72360677, -0.52573112, 0.44721365)285.48584, 629.8174, 86.05165
48generate(-0.44721362, 0.52573114, 0.72360676), (-0.8506508, -0.52573114), (-0.27639323, -0.85065079, 0.44721361)47.97695, 576.17756, 407.29168
49generate(0.3618034, 0.58778525, 0.72360679), (-0.26286554, 0.809017, -0.52573112), (-0.8944272, 2.0E-8, 0.44721359)-163.22296, 237.50889, 350.89141
50generate(0.67082038, -0.16245987, 0.7236068), (0.68819099, 0.5, -0.52573109), (-0.2763932, 0.8506508, 0.44721361)-56.24279, 81.83997, -5.20591
51generate(-0.3618034, 0.58778525, -0.72360679), (0.26286554, 0.809017, 0.52573112), (0.8944272, 2.0E-8, -0.44721359)363.11415, -144.89741, 134.02859
52generate(0.44721361, 0.52573113, -0.72360676), (0.8506508, 0.52573114), (0.27639324, -0.85065079, -0.44721361)182.00552, -91.25757, 490.1259
53generate(0.63819665, -0.26286554, -0.72360676), (0.26286554, -0.809017, 0.52573112), (-0.72360676, -0.52573112, -0.44721364)326.90291, 247.41111, 653.80588
54generate(-0.05278636, -0.68819097, -0.72360678), (-0.68819099, -0.5, 0.52573109), (-0.72360679, 0.52573109, -0.44721365)597.56306, 403.08002, 398.86837
55generate(-0.67082038, -0.16245987, -0.7236068), (-0.68819099, 0.5, 0.52573109), (0.2763932, 0.8506508, -0.44721361)619.94283, 160.62002, 77.62833
56generate(0.44721361, -0.85065078, 0.27639323), (-0.52573115, 0.85065079), (-0.72360677, -0.52573114, -0.44721361)273.26307, 163.67998, 653.80588
57generate(-0.67082038, -0.68819097, 0.2763932), (-0.16245988, 0.5, 0.8506508), (-0.72360681, 0.52573109, -0.44721361)504.95159, -45.62877, 398.86836
58generate(-0.86180342, 0.42532538, 0.27639319), (0.42532538, 0.309017, 0.85065082), (0.27639319, 0.85065082, -0.44721358)281.27417, -141.83745, 77.62832
59generate(0.13819656, 0.95105651, 0.27639322), (0.42532538, -0.30901699, 0.85065082), (0.89442722, 3.0E-8, -0.44721356)-88.6546, 8.01106, 134.02857
60generate(0.94721358, 0.16245987, 0.27639325), (-0.16245988, -0.5, 0.85065081), (0.27639326, -0.8506508, -0.44721358)-93.60573, 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

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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 / Entity ID: all / 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: 300 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
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 2406
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2406 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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