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- PDB-7c9x: Echovirus 3 F-particle -

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Basic information

Entry
Database: PDB / ID: 7c9x
TitleEchovirus 3 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 / 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 / symbiont entry into host cell / 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 / 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
MYRISTIC ACID / SPHINGOSINE / Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus E3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang, K. / 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 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 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 1.2Mar 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

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  • 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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  • Superimposition on EM map
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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)95,1956
Polymers94,6674
Non-polymers5282
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,711,716360
Polymers5,680,044240
Non-polymers31,672120
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
hetero molecules
x 5


  • icosahedral pentamer
  • 476 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)475,97630
Polymers473,33720
Non-polymers2,63910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 571 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)571,17236
Polymers568,00424
Non-polymers3,16712
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
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 5.71 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)5,711,716360
Polymers5,680,044240
Non-polymers31,672120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.67081502, -0.68819999, 0.27638376), (0.16247717, 0.4999968, 0.85064938), (-0.72360788, -0.52572233, 0.44722216)160.06577, -109.4462, 387.63857
3generate(0.13818254, -0.9510538, -0.27640958), (-0.4253064, -0.30902536, 0.85065728), (-0.8944384, 1.278E-5, -0.44719117)449.89818, 191.58259, 502.71259
4generate(0.13818254, -0.42530639, -0.8944384), (-0.9510538, -0.30902535, 1.278E-5), (-0.27640958, 0.85065727, -0.44719117)468.95868, 487.07482, 186.19367
5generate(0.67081502, 0.16247718, -0.72360789), (-0.68819999, 0.49999681, -0.52572233), (0.27638375, 0.85064937, 0.44722216)190.90632, 368.67027, -124.49979
6generate(-0.30901219, -0.95105808, -1.581E-5), (-0.95105808, 0.30901219, 2.176E-5), (-1.581E-5, 2.176E-5, -1)487.07962, 353.87882, 428.34704
7generate(-0.3618038, -0.2628555, -0.89442998), (-0.58779237, 0.80901183, 1.375E-5), (0.72360081, 0.52574408, -0.44720802)541.70091, 167.8352, 40.70355
8generate(0.36180514, 0.58778828, -0.72360347), (-0.26286395, 0.8090148, 0.5257353), (0.89442696, -4.47E-6, 0.44721405)165.84148, -14.78818, -74.3685
9generate(0.86181168, 0.42531247, 0.27638728), (-0.42531285, 0.309017, 0.85065709), (0.2763867, -0.85065727, 0.44720531)-121.07372, 58.38798, 242.15655
10generate(0.44722377, -0.52574688, 0.72358905), (-0.85064022, -1.61E-6, 0.52574826), (-0.27640933, -0.85064106, -0.44722216)77.46237, 286.23672, 552.85183
11generate(-0.63821961, 0.26286226, -0.7235877), (0.26286227, -0.80900963, -0.52574409), (-0.7235877, -0.52574408, 0.44722924)451.38359, 445.81493, 387.6374
12generate(0.13817558, 0.95105923, -0.27639437), (0.42531893, -0.30900863, -0.85065709), (-0.89443352, -1.571E-5, -0.44720093)39.9667, 372.63452, 502.71977
13generate(0.44721681, 0.52574083, 0.72359774), (0.85064565, 1.61E-6, -0.52573946), (-0.27640387, 0.8506448, -0.44721843)-149.14706, 144.78584, 186.20097
14generate(-0.13818039, -0.42531736, 0.89443352), (0.95105536, -0.30902055, -1.633E-5), (0.27640528, 0.85065354, 0.44720094)145.3911, 77.14802, -124.50079
15generate(-0.80901699, -0.58778525, 2.373E-5), (0.58778525, -0.809017, -1.919E-5), (3.047E-5, -1.58E-6, 1)516.53946, 263.19423, -0.00623
16generate(-0.0527682, 0.68819581, 0.72360351), (0.68819582, -0.50000255, 0.52572233), (0.72360351, 0.52572233, -0.44722924)-76.40543, 62.35748, 40.7122
17generate(-0.44718679, -3.74E-6, 0.89444059), (-3.73E-6, -1, -6.04E-6), (0.89444059, -6.05E-6, 0.44718679)120.3244, 431.02771, -74.36526
18generate(-0.94720449, -0.16247531, 0.27641531), (-0.16247531, -0.49999106, -0.85065311), (0.27641531, -0.85065311, 0.44719555)395.46519, 540.47097, 242.15158
19generate(-0.86181383, 0.42531129, -0.2763824), (0.42531128, 0.30902891, -0.85065354), (-0.2763824, -0.85065353, -0.44721508)368.78171, 239.4404, 552.8472
20generate(-0.3090218, 0.95105496, -4.9E-6), (0.95105495, 0.3090218, -6.74E-6), (-4.89E-6, -6.73E-6, -1)77.14963, -56.04999, 428.35082
21generate(0.94720531, -0.16246735, -0.27641718), (0.16247784, -0.5, 0.85064737), (-0.276411, -0.85064937, -0.44720531)105.59323, 106.0662, 552.85038
22generate(0.80901997, -0.58778117, -3.048E-5), (-0.58778116, -0.80901997, 9.9E-6), (-3.047E-5, 9.9E-6, -1)167.83985, 516.54018, 428.35275
23generate(0.44722378, -0.85064021, -0.27640934), (-0.52574687, -1.62E-6, -0.85064107), (0.72358905, 0.52574825, -0.44722216)361.65486, 511.00454, 40.70822
24generate(0.36180679, -0.58778223, -0.72360756), (0.26285142, 0.80901919, -0.52573481), (0.89442998, 1.314E-5, 0.44720801)419.1925, 97.10934, -74.37165
25generate(0.67081237, -0.16246801, -0.72361241), (0.68819768, 0.50000319, 0.52571927), (0.27639596, -0.85064737, 0.44721843)260.93771, -153.15631, 242.14961
26generate(-0.13817772, -0.95105767, 0.27639866), (0.42530796, -0.30901345, -0.85066082), (0.8944384, 1.216E-5, 0.44719117)391.0614, 372.63872, -74.36965
27generate(-0.44722111, -0.52574083, -0.72359509), (0.85064022, 8.72E-6, -0.52574826), (0.27641363, -0.8506448, 0.44721239)580.17631, 144.78737, 242.14654
28generate(0.13817558, 0.42531892, -0.89443352), (0.95105923, -0.30900864, -1.572E-5), (-0.27639436, -0.85065708, -0.44720094)285.63848, 77.14449, 552.84752
29generate(0.80901402, 0.58778934, -2.373E-5), (0.58778935, -0.80901402, -7.71E-6), (-2.372E-5, -7.71E-6, -1)-85.51081, 263.19025, 428.35509
30generate(0.63821828, -0.26285818, 0.72359035), (0.26285719, -0.809017, -0.5257353), (0.72359072, 0.5257348, -0.44723528)-20.35587, 445.81572, 40.71357
31generate(-0.44721948, 0.52574688, -0.72359171), (-0.85064565, -8.72E-6, 0.52573946), (0.27639956, 0.85064106, 0.44722819)353.56616, 286.2413, -124.5027
32generate(0.30901699, 0.95105652, 1.581E-5), (-0.95105652, 0.309017, 1.029E-5), (4.89E-6, -1.821E-5, 1)-56.05142, 353.8799, 0.00287
33generate(0.36180677, 0.26285142, 0.89442998), (-0.58778223, 0.80901919, 1.315E-5), (-0.72360756, -0.5257348, 0.44720802)-110.67178, 167.83156, 387.64422
34generate(-0.36180381, -0.58779236, 0.72360082), (-0.26285551, 0.80901183, 0.52574409), (-0.89442998, 1.376E-5, -0.44720801)265.18858, -14.79124, 502.71418
35generate(-0.86180953, -0.42531403, -0.27639158), (-0.42531404, 0.30900508, 0.85066082), (-0.27639159, 0.85066082, -0.44719555)552.1034, 58.39001, 186.18997
36generate(-0.36180811, 0.58777814, 0.72361022), (0.26285985, 0.80902216, -0.52572601), (-0.89442696, -3.85E-6, -0.44721405)11.83699, 97.105, 502.71861
37generate(-0.67081584, 0.16246549, 0.72360975), (0.68819746, 0.49999425, 0.52572807), (-0.27638806, 0.85065311, -0.44721239)170.09305, -153.15622, 186.19448
38generate(-0.94720613, 0.16246988, 0.27641288), (0.16246987, -0.50000894, 0.85064364), (0.27641287, 0.85064363, 0.44721508)325.43621, 106.07065, -124.50332
39generate(-0.809017, 0.58778525, 3.048E-5), (-0.58778525, -0.80901699, -1.57E-6), (2.372E-5, -1.919E-5, 1)263.18752, 516.54288, -0.00098
40generate(-0.44722112, 0.85064021, 0.27641363), (-0.52574083, 8.72E-6, -0.8506448), (-0.72359509, -0.52574825, 0.4472124)69.37254, 511.00181, 387.64349
41generate(0.94720531, 0.16247783, -0.27641102), (-0.16246734, -0.5, -0.85064938), (-0.27641717, 0.85064737, -0.44720531)35.56206, 540.47038, 186.20047
42generate(0.86181168, -0.42531285, 0.2763867), (0.42531248, 0.30901699, -0.85065728), (0.27638728, 0.85065708, 0.44720531)62.24706, 239.44351, -124.49861
43generate(0.309017, -0.95105652, 4.9E-6), (0.95105652, 0.30901699, -1.822E-5), (1.581E-5, 1.028E-5, 1)353.88063, -56.04683, -0.00562
44generate(0.05276473, -0.68819329, -0.72360616), (0.68820439, -0.5, 0.52571353), (-0.72359561, -0.52572807, 0.44723528)507.43509, 62.35697, 387.63436
45generate(0.44718679, 8.79E-6, -0.89444059), (8.8E-6, -1, -5.44E-6), (-0.89444059, -5.43E-6, -0.44718679)310.7034, 431.02488, 502.71605
46generate(-0.44721947, -0.85064565, 0.27639958), (0.52574687, -8.72E-6, 0.85064107), (-0.72359171, 0.52573946, 0.4472282)436.02409, -79.97669, 161.03032
47generate(-0.63821695, -0.26285309, -0.72359337), (-0.2628531, -0.80902436, 0.52572601), (-0.72359338, 0.52572601, 0.44724131)564.68263, 333.91963, 161.03076
48generate(0.05276472, 0.68820439, -0.72359561), (-0.68819328, -0.5, -0.52572807), (-0.72360617, 0.52571354, 0.44723528)210.80151, 584.18217, 161.0375
49generate(0.67081236, 0.68819768, 0.27639595), (-0.16246801, 0.5000032, -0.85064737), (-0.72361241, 0.52571928, 0.44721843)-136.56759, 324.9566, 161.04122
50generate(0.36180514, -0.26286394, 0.89442696), (0.58778827, 0.8090148, -4.47E-6), (-0.72360347, 0.5257353, 0.44721406)2.62761, -85.51615, 161.03678
51generate(-0.3618081, 0.26285986, -0.89442696), (0.58777814, 0.80902216, -3.86E-6), (0.72361022, -0.52572601, -0.44721406)428.4028, -85.51568, 267.30809
52generate(0.44721682, 0.85064565, -0.27640387), (0.52574083, 1.62E-6, 0.8506448), (0.72359775, -0.52573946, -0.44721843)-4.9937, -79.97842, 267.31461
53generate(0.63821828, 0.26285718, 0.72359072), (-0.26285817, -0.80901699, 0.52573481), (0.72359036, -0.5257353, -0.44723528)-133.65434, 333.91725, 267.31891
54generate(-0.05276124, -0.68820186, 0.72359827), (-0.68820186, -0.49999745, -0.52571927), (0.72359827, -0.52571928, -0.44724131)220.22552, 584.18158, 267.31505
55generate(-0.67081154, -0.68820021, -0.27639165), (-0.16247971, 0.50000575, -0.85064364), (0.72361054, -0.52571354, -0.4472282)567.59593, 324.95777, 267.30836
56generate(-0.13817774, 0.42530796, 0.8944384), (-0.95105767, -0.30901344, 1.218E-5), (0.27639867, -0.85066082, 0.44719117)-37.93116, 487.07322, 242.15776
57generate(-0.67081155, -0.1624797, 0.72361054), (-0.68820021, 0.50000575, -0.52571353), (-0.27639165, -0.85064363, -0.44722819)240.1218, 368.66651, 552.84987
58generate(-1, -5.05E-6), (-5.06E-6, 1, 1.148E-5), (1.148E-5, -1)431.02998, -0.00137, 428.34584
59generate(-0.67081584, 0.68819747, -0.27638805), (0.16246547, 0.49999425, 0.85065311), (0.72360975, 0.52572807, -0.4472124)270.96476, -109.44393, 40.70601
60generate(-0.13818039, 0.95105536, 0.27640528), (-0.42531736, -0.30902054, 0.85065354), (0.89443352, -1.633E-5, 0.44720093)-18.86916, 191.58472, -74.36455

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein VP1


Mass: 31761.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E3 / References: UniProt: A0A060BKX4
#2: Protein VP2


Mass: 29221.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E3 / References: UniProt: A0A0K0LDT3
#3: Protein VP3


Mass: 26281.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E3 / References: UniProt: A0A125RY26
#4: Protein VP4


Mass: 7402.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E3 / References: UniProt: A0A291S400

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#6: Chemical ChemComp-MYR / MYRISTIC ACID / 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

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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 E3 / Type: VIRUS
Details: Particles purified from the cell cultures innoculated with the live E3.
Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Echovirus E3
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 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 / 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
1RELION3particle selection
2RELION3image acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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