[English] 日本語
Yorodumi
- PDB-7c9y: Coxsackievirus B5 (CVB5) F-particle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c9y
TitleCoxsackievirus B5 (CVB5) F-particle
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Echovirus B / mature
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / 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 / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...RNA-protein covalent cross-linking / : / 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 / ribonucleoside triphosphate phosphatase activity / 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 / host cell cytoplasm / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont entry into host cell / 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 / proteolysis / RNA binding / ATP binding / metal ion binding / cytoplasm
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
MYRISTIC ACID / PALMITIC ACID / Genome polyprotein / VP4 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-30321
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-30321
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,1756
Polymers93,6904
Non-polymers4852
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,650,497360
Polymers5,621,410240
Non-polymers29,088120
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
  • 471 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)470,87530
Polymers468,45120
Non-polymers2,42410
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
  • 565 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)565,05036
Polymers562,14124
Non-polymers2,90912
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
  • 5.65 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)5,650,497360
Polymers5,621,410240
Non-polymers29,088120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.36180341, -0.26286552, -0.8944272), (0.58778526, 0.80901699, 4.0E-8), (0.72360679, -0.52573113, 0.44721358)434.68796, -96.06584, 85.9239
3generate(-0.67082036, 0.1624599, -0.72360681), (0.688191, 0.5, -0.52573107), (0.27639318, -0.85065079, -0.44721362)540.35928, 81.71845, 489.39819
4generate(-0.67082036, 0.68819099, 0.27639319), (0.16245991, 0.49999999, -0.85065081), (-0.72360681, -0.52573106, -0.44721362)170.97978, 287.66102, 652.83512
5generate(0.36180341, 0.58778525, 0.72360679), (-0.26286552, 0.80901699, -0.52573114), (-0.8944272, 4.0E-8, 0.44721359)-162.98062, 237.15624, 350.37041
6generate(-0.86180344, -0.42532534, 0.27639317), (-0.42532535, 0.309017, -0.85065084), (0.27639317, -0.85065083, -0.44721356)486.79909, 476.20082, 489.39819
7generate(-0.36180341, -0.26286552, 0.8944272), (-0.58778525, 0.809017, -4.0E-8), (-0.72360679, -0.52573113, -0.44721358)176.79152, 188.5398, 652.83512
8generate(0.36180341, -0.58778524, 0.72360679), (0.26286553, 0.809017, 0.52573113), (-0.8944272, -4.0E-8, 0.44721358)121.62499, -144.68227, 350.37043
9generate(0.30901699, -0.95105651, -4.0E-8), (0.95105652, 0.309017, 6.0E-8), (-5.0E-8, -6.0E-8, 1)397.53777, -62.96381, 3.0E-5
10generate(-0.44721363, -0.85065077, -0.27639326), (0.52573117, -0.85065078), (0.72360674, -0.52573116, 0.44721363)623.22778, 320.76304, 85.92391
11generate(0.809017, 0.58778524, 1.1E-7), (0.58778525, -0.809017, 4.0E-8), (1.1E-7, 4.0E-8, -1)-96.06585, 295.66019, 484.19997
12generate(0.63819669, 0.26286551, -0.72360673), (-0.26286553, -0.809017, -0.52573113), (-0.72360673, 0.52573113, -0.44721369)199.13803, 628.88226, 398.27612
13generate(-0.13819653, 0.42532534, -0.89442723), (-0.95105652, -0.30901699, -6.0E-8), (-0.27639323, 0.85065083, 0.44721352)389.12695, 547.16381, -5.19815
14generate(-0.44721362, 0.85065077, -0.27639326), (-0.52573117, 0.85065078), (0.72360674, 0.52573116, 0.44721362)211.34268, 163.43695, -168.63512
15generate(0.13819653, 0.95105651, 0.27639324), (0.42532535, -0.309017, 0.85065084), (0.89442723, 6.0E-8, -0.44721352)-88.52296, 7.99917, 133.82956
16generate(-0.94721356, -0.1624599, -0.27639329), (-0.1624599, -0.5, 0.85065081), (-0.27639329, 0.85065079, 0.44721356)577.66676, 196.53897, -5.19814
17generate(-0.63819669, 0.26286552, 0.72360673), (0.26286552, -0.809017, 0.52573113), (0.72360673, 0.52573113, 0.44721369)157.78248, 247.04376, -168.63512
18generate(0.44721348, 0.89442725), (-1), (0.89442725, -0.44721348)-82.71122, 484.2, 133.82956
19generate(0.80901699, -0.58778525, 1.1E-7), (-0.58778526, -0.80901699, -4.0E-8), (1.2E-7, -4.0E-8, -1)188.53977, 580.26583, 484.19999
20generate(-0.05278632, -0.68819099, -0.72360677), (-0.688191, -0.49999999, 0.52573108), (-0.72360677, 0.52573107, -0.44721369)596.67581, 402.48154, 398.27615
21generate(-0.13819653, -0.42532535, -0.89442723), (0.95105652, -0.309017, 6.0E-8), (-0.27639325, -0.85065083, 0.44721352)595.06948, 86.66221, 406.68698
22generate(-0.94721356, 0.1624599, -0.27639329), (0.1624599, -0.5, -0.8506508), (-0.27639329, -0.85065079, 0.44721356)499.00368, 529.76102, 406.68697
23generate(-0.44721362, 0.52573116, 0.72360674), (-0.85065078, -0.52573117), (-0.27639326, -0.85065077, 0.44721363)47.90571, 575.32207, 406.68694
24generate(0.67082036, 0.1624599, 0.72360681), (-0.688191, 0.5, 0.52573107), (-0.27639319, -0.85065079, 0.44721362)-134.82237, 160.38154, 406.68693
25generate(0.86180343, -0.42532535, -0.27639317), (0.42532535, 0.309017, 0.85065084), (-0.27639318, -0.85065083, 0.44721356)203.34344, -141.62686, 406.68695
26generate(0.05278631, 0.68819099, 0.72360677), (-0.688191, -0.5, 0.52573107), (0.72360677, -0.52573106, 0.44721369)-112.47581, 402.48154, 85.92386
27generate(0.94721356, 0.1624599, 0.27639329), (-0.16245991, -0.5, 0.8506508), (0.27639329, -0.85065079, -0.44721356)-93.46676, 196.53898, 489.39815
28generate(0.63819669, -0.26286553, -0.72360673), (0.26286552, -0.80901699, 0.52573114), (-0.72360673, -0.52573112, -0.44721369)326.41752, 247.04376, 652.83513
29generate(-0.44721348, -0.89442725), (-1), (-0.89442725, 0.44721348)566.91123, 484.19999, 350.37045
30generate(-0.80901699, 0.58778525, -1.1E-7), (-0.58778526, -0.809017, -4.0E-8), (-1.1E-7, 4.0E-8, 1)295.66023, 580.26583, 2.0E-5
31generate(-0.36180341, 0.26286553, 0.8944272), (0.58778526, 0.80901699, 3.0E-8), (-0.72360679, 0.52573112, -0.44721358)49.51203, -96.06583, 398.27612
32generate(0.67082037, -0.1624599, 0.72360681), (0.688191, 0.5, -0.52573108), (-0.27639319, 0.85065079, 0.44721362)-56.15928, 81.71846, -5.19818
33generate(0.67082036, -0.68819099, -0.27639319), (0.1624599, 0.5, -0.8506508), (0.72360681, 0.52573106, 0.44721363)313.22022, 287.66102, -168.63511
34generate(-0.36180341, -0.58778525, -0.72360679), (-0.26286552, 0.809017, -0.52573113), (0.8944272, -4.0E-8, -0.44721358)647.18062, 237.15624, 133.8296
35generate(-1), (1), (-1)484.2, 484.20001
36generate(0.44721362, -0.52573116, -0.72360674), (-0.85065078, -0.52573117), (0.27639326, 0.85065077, -0.44721362)436.29429, 575.32207, 77.51307
37generate(-0.67082037, -0.1624599, -0.72360681), (-0.68819099, 0.5, 0.52573108), (0.27639319, 0.85065079, -0.44721363)619.02236, 160.38154, 77.51308
38generate(-0.86180343, 0.42532535, 0.27639318), (0.42532536, 0.30901699, 0.85065084), (0.27639318, 0.85065083, -0.44721356)280.85655, -141.62686, 77.51306
39generate(0.13819653, 0.42532535, 0.89442723), (0.95105652, -0.309017, 6.0E-8), (0.27639324, 0.85065083, -0.44721352)-110.86948, 86.66222, 77.51303
40generate(0.94721356, -0.1624599, 0.27639329), (0.1624599, -0.5, -0.85065081), (0.27639329, 0.85065079, -0.44721356)-14.80368, 529.76102, 77.51304
41generate(-0.13819652, 0.95105651, -0.27639324), (-0.42532535, -0.309017, -0.85065084), (-0.89442723, 6.0E-8, 0.44721352)112.2214, 625.82685, 350.37042
42generate(0.309017, 0.95105651, -4.0E-8), (-0.95105652, 0.30901699, -6.0E-8), (-4.0E-8, 6.0E-8, 1)-62.96378, 397.53778
43generate(0.67082037, 0.68819099, -0.27639319), (-0.1624599, 0.5, 0.85065081), (0.72360681, -0.52573107, 0.44721362)-20.00186, -45.56102, 85.92387
44generate(0.44721363, 0.52573116, -0.72360674), (0.85065078, 0.52573117), (0.27639325, -0.85065077, -0.44721362)181.73526, -91.12207, 489.39817
45generate(-0.05278631, 0.68819099, -0.72360677), (0.688191, -0.50000001, -0.52573107), (-0.72360678, -0.52573106, -0.44721369)263.45373, 323.81845, 652.83513
46generate(-0.36180341, 0.58778525, -0.72360679), (0.26286553, 0.80901699, 0.52573114), (0.8944272, 3.0E-8, -0.44721359)362.575, -144.68227, 133.82959
47generate(-0.30901699, 0.95105651, 4.0E-8), (0.95105653, 0.30901699, 6.0E-8), (4.0E-8, 6.0E-8, -1)86.66222, -62.96381, 484.19999
48generate(0.44721363, 0.85065077, 0.27639326), (0.52573117, -0.85065078), (-0.72360674, 0.52573116, -0.44721362)-139.02778, 320.76304, 398.2761
49generate(0.86180343, 0.42532535, -0.27639318), (-0.42532536, 0.30901699, -0.85065084), (-0.27639317, 0.85065083, 0.44721356)-2.59909, 476.20083, -5.19818
50generate(0.36180341, 0.26286552, -0.8944272), (-0.58778525, 0.809017, -3.0E-8), (0.7236068, 0.52573112, 0.44721358)307.40848, 188.5398, -168.63511
51generate(0.44721362, -0.85065077, 0.27639326), (-0.52573117, 0.85065078), (-0.72360674, -0.52573116, -0.44721363)272.85732, 163.43695, 652.83513
52generate(-0.13819653, -0.95105651, -0.27639324), (0.42532535, -0.30901699, 0.85065084), (-0.89442723, -6.0E-8, 0.44721352)572.72296, 7.99917, 350.37045
53generate(-0.809017, -0.58778525, -1.1E-7), (0.58778526, -0.80901699, 4.0E-8), (-1.2E-7, -3.0E-8, 1)580.26585, 295.66019, 4.0E-5
54generate(-0.63819669, -0.26286552, 0.72360673), (-0.26286553, -0.80901699, -0.52573114), (0.72360673, -0.52573112, 0.44721369)285.06197, 628.88226, 85.92388
55generate(0.13819652, -0.42532535, 0.89442723), (-0.95105653, -0.30901699, -6.0E-8), (0.27639324, -0.85065083, -0.44721352)95.07305, 547.16381, 489.39816
56generate(0.05278631, -0.68819099, 0.72360677), (0.688191, -0.5, -0.52573108), (0.72360677, 0.52573106, 0.44721369)220.74627, 323.81845, -168.63512
57generate(0.13819652, -0.95105651, 0.27639324), (-0.42532536, -0.30901699, -0.85065084), (0.89442723, -6.0E-8, -0.44721352)371.9786, 625.82685, 133.82958
58generate(-0.309017, -0.95105651, 4.0E-8), (-0.95105652, 0.309017, -6.0E-8), (5.0E-8, -6.0E-8, -1)547.16378, 397.53778, 484.20001
59generate(-0.67082037, -0.68819098, 0.27639319), (-0.1624599, 0.50000001, 0.8506508), (-0.72360681, 0.52573106, -0.44721363)504.20185, -45.56102, 398.27614
60generate(-0.44721362, -0.52573116, 0.72360674), (0.85065078, 0.52573117), (-0.27639326, 0.85065077, 0.44721362)302.46473, -91.12207, -5.19816

-
Components

-
Protein , 4 types, 4 molecules ABCD

#1: Protein VP1


Mass: 31574.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B5 / References: UniProt: S5PN91
#2: Protein VP2


Mass: 28626.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B5 / References: UniProt: A0A1U9XQA4*PLUS
#3: Protein VP3


Mass: 26163.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B5 / References: UniProt: I7AVS5
#4: Protein VP4


Mass: 7326.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B5 / References: UniProt: F5BZJ3*PLUS

-
Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Coxsackievirus B5 / Type: VIRUS
Details: Particles purified from the cell cultures innoculated with the live CB5.
Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Coxsackievirus B5
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 %

-
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

-
Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2RELION3image acquisition
4RELION3CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
11RELIONfinal Euler assignment
12RELIONclassification
13RELION33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8890 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more