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- PDB-7c81: E30 F-particle in complex with 6C5 -

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Basic information

Entry
Database: PDB / ID: 7c81
TitleE30 F-particle in complex with 6C5
Components
  • Heavy chain
  • Light chain
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS/IMMUNE SYSTEM / MAb / 6C5 / E30 / VIRUS-IMMUNE SYSTEM complex
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 / viral capsid ...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 / RNA helicase activity / DNA replication / 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 / 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
SPHINGOSINE / Genome polyprotein / Genome polyprotein / Genome polyprotein / VP4
Similarity search - Component
Biological speciesEchovirus E30
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang, K. / Zheng, B. / Zhang, L. / Cui, L. / Su, X. / Zhang, Q. / Guo, Y. / Zhu, L. / 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: Serotype specific epitopes identified by neutralizing antibodies underpin immunogenic differences in Enterovirus B.
Authors: Kang Wang / Binyang Zheng / Li Zhang / Lunbiao Cui / Xuan Su / Qian Zhang / Zhenxi Guo / Yu Guo / Wei Zhang / Ling Zhu / Fengcai Zhu / Zihe Rao / Xiangxi Wang /
Abstract: Echovirus 30 (E30), a serotype of Enterovirus B (EV-B), recently emerged as a major causative agent of aseptic meningitis worldwide. E30 is particularly devastating in the neonatal population and ...Echovirus 30 (E30), a serotype of Enterovirus B (EV-B), recently emerged as a major causative agent of aseptic meningitis worldwide. E30 is particularly devastating in the neonatal population and currently no vaccine or antiviral therapy is available. Here we characterize two highly potent E30-specific monoclonal antibodies, 6C5 and 4B10, which efficiently block binding of the virus to its attachment receptor CD55 and uncoating receptor FcRn. Combinations of 6C5 and 4B10 augment the sum of their individual anti-viral activities. High-resolution structures of E30-6C5-Fab and E30-4B10-Fab define the location and nature of epitopes targeted by the antibodies. 6C5 and 4B10 engage the capsid loci at the north rim of the canyon and in-canyon, respectively. Notably, these regions exhibit antigenic variability across EV-Bs, highlighting challenges in development of broad-spectrum antibodies. Our structures of these neutralizing antibodies of E30 are instructive for development of vaccines and therapeutics against EV-B infections.
History
DepositionMay 28, 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

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-30304
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-30304
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
L: Light chain
H: Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8977
Polymers142,5976
Non-polymers2991
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
L: Light chain
H: Heavy chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,573,818420
Polymers8,555,849360
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
L: Light chain
H: Heavy chain
hetero molecules
x 5


  • icosahedral pentamer
  • 714 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)714,48535
Polymers712,98730
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP2
C: VP3
D: VP4
L: Light chain
H: Heavy chain
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 857 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)857,38242
Polymers855,58536
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
L: Light chain
H: Heavy chain
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 8.57 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)8,573,818420
Polymers8,555,849360
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.95105651, -3.0E-8), (0.95105652, 0.309017, 3.0E-8), (-3.0E-8, -4.0E-8, 1)
3generate(-0.809017, -0.58778525, -7.0E-8), (0.58778526, -0.80901699, 2.0E-8), (-8.0E-8, -2.0E-8, 1)
4generate(-0.80901699, 0.58778525, -7.0E-8), (-0.58778526, -0.809017, -3.0E-8), (-7.0E-8, 3.0E-8, 1)
5generate(0.309017, 0.95105651, -2.0E-8), (-0.95105652, 0.30901699, -4.0E-8), (-2.0E-8, 4.0E-8, 1)
6generate(-0.63819654, 0.26286557, -0.72360684), (0.26286558, -0.809017, -0.52573111), (-0.72360685, -0.5257311, 0.44721354)
7generate(0.05278646, 0.68819093, -0.72360681), (-0.68819094, -0.50000001, -0.52573114), (-0.72360681, 0.52573114, 0.44721354)
8generate(0.67082041, 0.16245981, -0.72360679), (-0.68819094, 0.49999999, -0.52573114), (0.27639322, 0.85065081, 0.44721358)
9generate(0.36180339, -0.58778525, -0.7236068), (0.26286558, 0.80901699, -0.5257311), (0.89442719, -2.0E-8, 0.4472136)
10generate(-0.44721358, -0.52573108, -0.72360683), (0.85065083, -0.52573108), (0.27639316, -0.85065082, 0.44721358)
11generate(-0.05278646, 0.68819094, 0.72360681), (0.68819094, -0.5, 0.52573114), (0.72360681, 0.52573114, -0.44721354)
12generate(0.63819654, 0.26286558, 0.72360684), (-0.26286559, -0.80901699, 0.5257311), (0.72360684, -0.5257311, -0.44721354)
13generate(0.44721358, -0.52573107, 0.72360683), (-0.85065083, 0.52573108), (-0.27639316, -0.85065083, -0.44721358)
14generate(-0.3618034, -0.58778525, 0.7236068), (-0.26286557, 0.809017, 0.52573111), (-0.89442719, -3.0E-8, -0.4472136)
15generate(-0.67082041, 0.16245982, 0.72360679), (0.68819095, 0.5, 0.52573114), (-0.27639321, 0.85065081, -0.44721358)
16generate(-0.309017, -0.95105651, 2.0E-8), (-0.95105652, 0.309017, -3.0E-8), (3.0E-8, -4.0E-8, -1)
17generate(-1), (1), (-1)
18generate(-0.30901699, 0.95105651, 3.0E-8), (0.95105652, 0.30901699, 4.0E-8), (2.0E-8, 3.0E-8, -1)
19generate(0.809017, 0.58778525, 7.0E-8), (0.58778525, -0.809017, 2.0E-8), (7.0E-8, 2.0E-8, -1)
20generate(0.80901699, -0.58778525, 7.0E-8), (-0.58778526, -0.80901699, -2.0E-8), (8.0E-8, -2.0E-8, -1)
21generate(-0.13819665, -0.95105651, 0.27639318), (0.42532544, -0.30901699, -0.8506508), (0.89442717, -4.0E-8, 0.44721364)
22generate(-0.94721362, -0.16245981, 0.27639315), (-0.16245981, -0.5, -0.85065082), (0.27639314, -0.85065081, 0.44721362)
23generate(-0.44721358, 0.85065083, 0.27639317), (-0.52573108, -0.85065083), (-0.72360683, -0.52573107, 0.44721358)
24generate(0.67082041, 0.68819094, 0.27639321), (-0.16245981, 0.49999999, -0.85065082), (-0.72360679, 0.52573114, 0.44721358)
25generate(0.86180338, -0.42532543, 0.27639322), (0.42532544, 0.30901699, -0.8506508), (0.27639322, 0.85065079, 0.44721362)
26generate(-0.36180339, 0.58778525, 0.7236068), (0.26286559, 0.80901699, -0.5257311), (-0.89442719, 2.0E-8, -0.4472136)
27generate(0.44721358, 0.52573108, 0.72360683), (0.85065083, -0.52573108), (-0.27639317, 0.85065082, -0.44721357)
28generate(0.63819654, -0.26286557, 0.72360684), (0.26286557, -0.809017, -0.52573111), (0.72360684, 0.5257311, -0.44721353)
29generate(-0.05278646, -0.68819093, 0.72360681), (-0.68819095, -0.5, -0.52573114), (0.72360682, -0.52573114, -0.44721354)
30generate(-0.67082041, -0.16245981, 0.72360679), (-0.68819094, 0.5, -0.52573114), (-0.27639321, -0.85065082, -0.44721358)
31generate(-0.44721357, 0.52573107, -0.72360683), (-0.85065083, 0.52573108), (0.27639317, 0.85065083, 0.44721358)
32generate(0.3618034, 0.58778525, -0.7236068), (-0.26286558, 0.80901699, 0.52573111), (0.89442719, 2.0E-8, 0.4472136)
33generate(0.67082041, -0.16245982, -0.72360679), (0.68819094, 0.50000001, 0.52573114), (0.27639321, -0.85065081, 0.44721357)
34generate(0.05278646, -0.68819094, -0.72360682), (0.68819094, -0.49999999, 0.52573114), (-0.72360682, -0.52573114, 0.44721353)
35generate(-0.63819654, -0.26286558, -0.72360684), (-0.26286558, -0.80901699, 0.5257311), (-0.72360684, 0.5257311, 0.44721354)
36generate(0.94721362, -0.16245981, -0.27639315), (0.16245981, -0.49999999, 0.85065082), (-0.27639315, -0.85065081, -0.44721362)
37generate(0.13819664, -0.95105651, -0.27639318), (-0.42532544, -0.30901699, 0.8506508), (-0.89442717, -4.0E-8, -0.44721364)
38generate(-0.86180338, -0.42532544, -0.27639322), (-0.42532544, 0.309017, 0.8506508), (-0.27639322, 0.85065078, -0.44721362)
39generate(-0.67082041, 0.68819093, -0.27639321), (0.16245981, 0.5, 0.85065082), (0.72360679, 0.52573114, -0.44721358)
40generate(0.44721358, 0.85065082, -0.27639317), (0.52573108, 0.85065083), (0.72360683, -0.52573108, -0.44721358)
41generate(-0.13819665, 0.42532544, 0.89442717), (-0.95105652, -0.30901699, -4.0E-8), (0.27639318, -0.85065078, 0.44721364)
42generate(0.36180339, 0.26286558, 0.89442719), (-0.58778525, 0.809017, -2.0E-8), (-0.7236068, -0.5257311, 0.4472136)
43generate(0.36180339, -0.26286557, 0.89442719), (0.58778526, 0.80901699, 2.0E-8), (-0.7236068, 0.5257311, 0.44721361)
44generate(-0.13819665, -0.42532543, 0.89442717), (0.95105652, -0.309017, 3.0E-8), (0.27639318, 0.85065079, 0.44721365)
45generate(-0.44721367, 0.89442716), (-1), (0.89442716, 0.44721367)
46generate(-0.44721358, -0.85065082, 0.27639316), (0.52573108, 0.85065083), (-0.72360684, 0.52573108, 0.44721358)
47generate(-0.94721362, 0.16245982, 0.27639315), (0.16245981, -0.5, 0.85065081), (0.27639315, 0.85065082, 0.44721362)
48generate(-0.13819664, 0.95105651, 0.27639318), (-0.42532544, -0.30901699, 0.85065079), (0.89442717, 4.0E-8, 0.44721364)
49generate(0.86180338, 0.42532544, 0.27639322), (-0.42532544, 0.309017, 0.85065079), (0.27639322, -0.85065079, 0.44721361)
50generate(0.67082041, -0.68819094, 0.27639321), (0.16245982, 0.50000001, 0.85065082), (-0.72360679, -0.52573114, 0.44721357)
51generate(0.94721362, 0.16245981, -0.27639315), (-0.16245982, -0.50000001, -0.85065082), (-0.27639314, 0.85065081, -0.44721361)
52generate(0.44721358, -0.85065083, -0.27639317), (-0.52573108, -0.85065083), (0.72360684, 0.52573107, -0.44721357)
53generate(-0.67082041, -0.68819094, -0.27639321), (-0.16245981, 0.5, -0.85065081), (0.72360679, -0.52573114, -0.44721358)
54generate(-0.86180338, 0.42532543, -0.27639322), (0.42532545, 0.30901699, -0.85065079), (-0.27639322, -0.85065079, -0.44721362)
55generate(0.13819665, 0.95105651, -0.27639318), (0.42532544, -0.309017, -0.85065079), (-0.89442717, 4.0E-8, -0.44721364)
56generate(-0.36180339, 0.26286557, -0.89442719), (0.58778526, 0.809017, 3.0E-8), (0.7236068, -0.5257311, -0.44721361)
57generate(0.13819665, 0.42532543, -0.89442717), (0.95105652, -0.30901699, 4.0E-8), (-0.27639318, -0.85065079, -0.44721365)
58generate(0.44721367, -0.89442716), (-1), (-0.89442716, -0.44721367)
59generate(0.13819665, -0.42532544, -0.89442717), (-0.95105652, -0.309017, -3.0E-8), (-0.27639317, 0.85065079, -0.44721364)
60generate(-0.36180339, -0.26286558, -0.89442719), (-0.58778525, 0.80901699, -2.0E-8), (0.72360681, 0.5257311, -0.4472136)

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Components

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Protein , 4 types, 4 molecules ABCD

#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

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Antibody , 2 types, 2 molecules LH

#5: Antibody Light chain /


Mass: 23490.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#6: Antibody Heavy chain


Mass: 23332.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2

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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

Component
IDNameTypeEntity IDParent-IDSource
1E30 F-particle in complex with 6C5COMPLEX#1-#60MULTIPLE SOURCES
2E30 F-particle in complex with 6C5COMPLEX#1-#41NATURAL
3E30 F-particle in complex with 6C5COMPLEX#5-#61NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Echovirus E3041846
33Mus musculus (house mouse)10090
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NONOSEROTYPEVIRION
22
33
Buffer solutionpH: 7.4 / Details: pH = 7.4 PBS purchased from Thermo Fisher.
Buffer componentName: PBS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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
IDNameVersionCategoryDetails
1RELION3particle selection
2RELION3image acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting1.13.1
12RELION33D reconstruction
13PHENIXmodel refinement1.14
CTF correctionType: NONE
Particle selectionNum. of particles selected: 16488
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10127 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: CC

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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

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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

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