[English] 日本語
Yorodumi
- PDB-7c9w: E30 F-particle in complex with CD55 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c9w
TitleE30 F-particle in complex with CD55
Components
  • Complement decay-accelerating factor
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Echovirus 30 / mature / attachement receptor
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / complement activation, classical pathway / COPI-mediated anterograde transport / side of membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / 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 / positive regulation of T cell cytokine production / host cell cytoplasmic vesicle membrane / viral capsid / host cell / nucleoside-triphosphate phosphatase / virus receptor activity / positive regulation of cytosolic calcium ion concentration / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / membrane raft / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / Golgi membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / innate immune response / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / : / Neutrophil degranulation / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Picornavirus coat protein VP4 superfamily / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Jelly Rolls - #20 ...: / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Picornavirus coat protein VP4 superfamily / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Jelly Rolls - #20 / 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 / Ribbon / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / SPHINGOSINE / Genome polyprotein / Genome polyprotein / Complement decay-accelerating factor / Genome polyprotein / VP4
Similarity search - Component
Biological speciesHomo sapiens (human)
Echovirus E30
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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 1.1Aug 12, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 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 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _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-30319
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-30319
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
E: Complement decay-accelerating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4007
Polymers116,8725
Non-polymers5282
Water00
1
A: VP1
B: VP2
C: VP3
D: VP4
E: Complement decay-accelerating factor
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,044,000420
Polymers7,012,329300
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
E: Complement decay-accelerating factor
hetero molecules
x 5


  • icosahedral pentamer
  • 587 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)587,00035
Polymers584,36125
Non-polymers2,63910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
E: Complement decay-accelerating factor
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 704 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)704,40042
Polymers701,23330
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
E: Complement decay-accelerating factor
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 7.04 MDa, 300 polymers
Theoretical massNumber of molelcules
Total (without water)7,044,000420
Polymers7,012,329300
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(0.809017, -0.5, 0.30901699), (0.5, 0.309017, -0.80901699), (0.30901699, 0.80901699, 0.5)75.2855, 197.1, -121.8145
3generate(0.5, -0.309017, 0.80901699), (0.309017, -0.80901699, -0.5), (0.80901699, 0.5, -0.309017)394.2
4generate(0.5, 0.30901699, 0.809017), (-0.30901699, -0.809017, 0.5), (0.80901699, -0.5, -0.30901699)-121.8145, 318.9145, 197.1
5generate(0.80901699, 0.5, 0.309017), (-0.5, 0.30901699, 0.80901699), (0.30901699, -0.809017, 0.5)-121.8145, 75.2855, 197.1
6generate(-0.5, 0.30901699, 0.80901699), (0.309017, -0.80901699, 0.50000001), (0.809017, 0.49999999, 0.30901699)75.2855, 197.1, -121.8145
7generate(1), (1), (1)
8generate(0.5, 0.309017, -0.80901699), (0.309017, 0.80901699, 0.5), (0.80901699, -0.5, 0.309017)197.1, -121.8145, 75.2855
9generate(0.309017, -0.80901699, -0.5), (0.80901699, 0.5, -0.30901699), (0.5, -0.30901699, 0.809017)394.2
10generate(-0.30901699, -0.809017, 0.5), (0.809017, -0.5, -0.30901699), (0.5, 0.30901699, 0.80901699)318.9145, 197.1, -121.8145
11generate(0.30901699, -0.809017, -0.49999999), (-0.80901699, -0.5, 0.30901699), (-0.50000001, 0.309017, -0.80901699)394.2, 394.20001, 394.2
12generate(-0.30901699, -0.80901699, 0.5), (-0.809017, 0.5, 0.30901699), (-0.5, -0.30901699, -0.809017)318.9145, 197.1, 516.0145
13generate(-0.5, 0.309017, 0.80901699), (-0.309017, 0.80901699, -0.5), (-0.80901699, -0.5, -0.309017)75.2855, 197.1, 516.0145
14generate(1), (-1), (-1)394.2, 394.2
15generate(0.5, 0.30901699, -0.809017), (-0.309017, -0.80901699, -0.5), (-0.809017, 0.5, -0.309017)197.1, 516.01451, 318.9145
16generate(-0.80901699, 0.50000001, -0.309017), (0.49999999, 0.30901699, -0.809017), (-0.30901699, -0.80901699, -0.5)318.9145, 197.1, 516.0145
17generate(-0.5, 0.309017, -0.809017), (0.30901699, -0.809017, -0.5), (-0.80901699, -0.5, 0.309017)394.2, 394.20001, 394.2
18generate(-0.5, -0.309017, -0.80901699), (-0.309017, -0.80901699, 0.5), (-0.80901699, 0.5, 0.309017)516.0145, 318.9145, 197.1
19generate(-0.809017, -0.5, -0.30901699), (-0.5, 0.309017, 0.80901699), (-0.309017, 0.809017, -0.5)516.0145, 75.2855, 197.1
20generate(-1), (1), (-1)394.2, 394.2
21generate(-1), (-1), (1)394.2, 394.2
22generate(-0.5, -0.309017, 0.80901699), (-0.30901699, -0.80901699, -0.5), (0.809017, -0.5, 0.30901699)197.1, 516.0145, 75.2855
23generate(-0.309017, 0.80901699, 0.5), (-0.80901699, -0.5, 0.309017), (0.5, -0.309017, 0.80901699)394.2
24generate(0.30901699, 0.809017, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.809017)75.2855, 197.1, -121.8145
25generate(0.5, -0.30901699, -0.80901699), (-0.30901699, 0.809017, -0.5), (0.80901699, 0.5, 0.309017)318.9145, 197.1, -121.8145
26generate(-0.309017, 0.80901699, -0.50000001), (-0.809017, -0.49999999, -0.30901699), (-0.5, 0.30901699, 0.80901699)197.1, 516.0145, 75.2855
27generate(-1), (-1), (1)394.2, 394.2
28generate(-0.309017, -0.80901699, -0.5), (-0.80901699, 0.5, -0.309017), (0.5, 0.309017, -0.80901699)516.0145, 318.9145, 197.1
29generate(-0.80901699, -0.5, 0.30901699), (-0.5, 0.30901699, -0.809017), (0.309017, -0.80901699, -0.5)394.2, 394.20001, 394.2
30generate(-0.809017, 0.5, 0.30901699), (-0.5, -0.30901699, -0.80901699), (-0.30901699, -0.809017, 0.5)197.1, 516.0145, 318.9145
31generate(0.80901699, 0.5, -0.30901699), (0.50000001, -0.309017, 0.80901699), (0.30901699, -0.809017, -0.49999999)394.2
32generate(0.809017, -0.5, -0.30901699), (0.5, 0.30901699, 0.809017), (-0.30901699, -0.80901699, 0.5)197.1, -121.8145, 318.9145
33generate(0.309017, -0.80901699, 0.5), (0.80901699, 0.5, 0.309017), (-0.5, 0.309017, 0.80901699)197.1, -121.8145, 75.2855
34generate(1), (1), (1)
35generate(0.309017, 0.80901699, 0.5), (0.809017, -0.5, 0.309017), (0.5, 0.30901699, -0.809017)-121.8145, 75.2855, 197.1
36generate(-0.49999999, -0.30901699, 0.809017), (0.30901699, 0.80901699, 0.5), (-0.80901699, 0.50000001, -0.309017)197.1, -121.8145, 318.9145
37generate(-0.30901699, 0.809017, 0.5), (0.80901699, 0.5, -0.309017), (-0.5, 0.309017, -0.809017)394.2
38generate(0.309017, 0.80901699, -0.5), (0.80901699, -0.5, -0.309017), (-0.5, -0.309017, -0.80901699)75.2855, 197.1, 516.0145
39generate(0.5, -0.309017, -0.80901699), (0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.30901699)318.9145, 197.1, 516.0145
40generate(-1), (1), (-1)394.2, 394.2
41generate(1), (-1), (-1)394.2, 394.2
42generate(0.30901699, 0.80901699, 0.5), (-0.809017, 0.5, -0.30901699), (-0.5, -0.309017, 0.80901699)-121.8145, 318.9145, 197.1
43generate(0.80901699, 0.5, -0.309017), (-0.5, 0.309017, -0.80901699), (-0.309017, 0.80901699, 0.5)394.2
44generate(0.80901699, -0.5, -0.30901699), (-0.5, -0.30901699, -0.809017), (0.30901699, 0.809017, -0.5)197.1, 516.0145, 75.2855
45generate(0.30901699, -0.809017, 0.5), (-0.80901699, -0.5, -0.309017), (0.5, -0.30901699, -0.80901699)197.1, 516.01451, 318.9145
46generate(0.809017, 0.49999999, 0.30901699), (0.5, -0.30901699, -0.80901699), (-0.309017, 0.80901699, -0.50000001)-121.8145, 318.9145, 197.1
47generate(1), (-1), (-1)394.20001, 394.2
48generate(0.80901699, -0.5, 0.309017), (-0.5, -0.309017, 0.80901699), (-0.309017, -0.80901699, -0.5)75.2855, 197.1, 516.0145
49generate(0.5, -0.30901699, 0.809017), (-0.309017, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699)394.2
50generate(0.5, 0.30901699, 0.80901699), (0.30901699, 0.809017, -0.5), (-0.809017, 0.5, 0.30901699)-121.8145, 75.2855, 197.1
51generate(-0.50000001, 0.309017, -0.80901699), (-0.30901699, 0.809017, 0.49999999), (0.80901699, 0.5, -0.30901699)394.2
52generate(-0.5, -0.30901699, -0.809017), (0.30901699, 0.80901699, -0.5), (0.809017, -0.5, -0.30901699)516.0145, 75.2855, 197.1
53generate(-0.80901699, -0.5, -0.309017), (0.5, -0.309017, -0.80901699), (0.309017, -0.80901699, 0.5)516.0145, 318.9145, 197.1
54generate(-1), (-1), (1)394.2, 394.2
55generate(-0.809017, 0.5, -0.309017), (-0.5, -0.30901699, 0.809017), (0.309017, 0.80901699, 0.5)318.9145, 197.1, -121.8145
56generate(-0.30901699, -0.80901699, -0.5), (0.80901699, -0.50000001, 0.309017), (-0.49999999, -0.30901699, 0.809017)516.0145, 75.2855, 197.1
57generate(-0.80901699, -0.5, 0.309017), (0.5, -0.309017, 0.809017), (-0.30901699, 0.809017, 0.5)394.2
58generate(-0.80901699, 0.5, 0.309017), (0.5, 0.309017, 0.80901699), (0.309017, 0.80901699, -0.5)197.1, -121.8145, 75.2855
59generate(-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.30901699), (0.5, -0.309017, -0.80901699)197.1, -121.8145, 318.9145
60generate(-1), (1), (-1)394.2, 394.2

-
Components

-
Protein , 5 types, 5 molecules ABCDE

#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: 7437.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E30 / References: UniProt: Q33C85, UniProt: Q8QWB2*PLUS
#5: Protein Complement decay-accelerating factor


Mass: 21307.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD55, CR, DAF / Production host: Homo sapiens (human) / References: UniProt: P08174

-
Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-SPH / SPHINGOSINE


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


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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1E30 F-particle in complex with CD55COMPLEX#1-#50MULTIPLE SOURCES
2E30 F-particle in complex with FcRnCOMPLEX#1-#41NATURAL
3CD55 or DAF (decay-accelerating factor)COMPLEX#51RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Echovirus E3041846
31Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
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
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
1RELIONparticle selection
2RELION3image acquisition
4RELIONCTF correction
7UCSF Chimeramodel fitting
10RELIONfinal Euler assignment
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1016 / 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