[English] 日本語
Yorodumi
- PDB-5xs5: Structure of Coxsackievirus A6 (CVA6) virus procapsid particle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xs5
TitleStructure of Coxsackievirus A6 (CVA6) virus procapsid particle
Components(Genome polyprotein) x 3
KeywordsVIRUS / Coxsackievirus A6 / procapsid / icosahedral
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / 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 / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / 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 ...Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / 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) / 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 / 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
Biological speciesCoxsackievirus A6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZheng, Q.B. / He, M.Z. / Xu, L.F. / Yu, H. / Cheng, T. / Li, S.W.
Funding support China, United States, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670933 China
National Natural Science Foundation of China81401669 China
National Science and Technology Major Projects for Major New Drugs Innovation and Development2017ZX09101005-005-003 China
National Science and Technology Major Project of Infectious Diseases2017ZX10304402-002-003 China
Natural Science Foundation of Fujian Province2015J05073 China
National Institutes of HealthR37-GM33050 United States
CitationJournal: Nat Commun / Year: 2017
Title: Atomic structures of Coxsackievirus A6 and its complex with a neutralizing antibody.
Authors: Longfa Xu / Qingbing Zheng / Shaowei Li / Maozhou He / Yangtao Wu / Yongchao Li / Rui Zhu / Hai Yu / Qiyang Hong / Jie Jiang / Zizhen Li / Shuxuan Li / Huan Zhao / Lisheng Yang / Wangheng ...Authors: Longfa Xu / Qingbing Zheng / Shaowei Li / Maozhou He / Yangtao Wu / Yongchao Li / Rui Zhu / Hai Yu / Qiyang Hong / Jie Jiang / Zizhen Li / Shuxuan Li / Huan Zhao / Lisheng Yang / Wangheng Hou / Wei Wang / Xiangzhong Ye / Jun Zhang / Timothy S Baker / Tong Cheng / Z Hong Zhou / Xiaodong Yan / Ningshao Xia /
Abstract: Coxsackievirus A6 (CVA6) has recently emerged as a major cause of hand, foot and mouth disease in children worldwide but no vaccine is available against CVA6 infections. Here, we demonstrate the ...Coxsackievirus A6 (CVA6) has recently emerged as a major cause of hand, foot and mouth disease in children worldwide but no vaccine is available against CVA6 infections. Here, we demonstrate the isolation of two forms of stable CVA6 particles-procapsid and A-particle-with excellent biochemical stability and natural antigenicity to serve as vaccine candidates. Despite the presence (in A-particle) or absence (in procapsid) of capsid-RNA interactions, the two CVA6 particles have essentially identical atomic capsid structures resembling the uncoating intermediates of other enteroviruses. Our near-atomic resolution structure of CVA6 A-particle complexed with a neutralizing antibody maps an immune-dominant neutralizing epitope to the surface loops of VP1. The structure-guided cell-based inhibition studies further demonstrate that these loops could serve as excellent targets for designing anti-CVA6 vaccines.Coxsackievirus A6 (CVA6) causes hand, foot and mouth disease in children. Here the authors present the CVA6 procapsid and A-particle cryo-EM structures and identify an immune-dominant neutralizing epitope, which can be exploited for vaccine development.
History
DepositionJun 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_software / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_software.name / _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-6752
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6752
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)95,3813
Polymers95,3813
Non-polymers00
Water0
1
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)5,722,850180
Polymers5,722,850180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area10980 Å2
ΔGint-69 kcal/mol
Surface area26630 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 5


  • icosahedral pentamer
  • 477 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)476,90415
Polymers476,90415
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 6


  • icosahedral 23 hexamer
  • 572 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)572,28518
Polymers572,28518
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: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 60


  • crystal asymmetric unit, crystal frame
  • 5.72 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)5,722,850180
Polymers5,722,850180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.809017, -0.30901699, -0.5), (-0.30901699, 0.5, -0.80901699), (0.5, 0.80901699, 0.309017)231.26651, 374.19707, -142.93056
3generate(0.5, -0.80901699, -0.309017), (-0.80901699, -0.309017, -0.5), (0.309017, 0.5, -0.80901699)374.19707, 605.46358, 231.26651
4generate(0.5, -0.809017, 0.30901699), (-0.80901699, -0.30901699, 0.5), (-0.30901699, -0.5, -0.809017)231.26651, 374.19707, 605.46358
5generate(0.80901699, -0.309017, 0.5), (-0.30901699, 0.5, 0.809017), (-0.5, -0.80901699, 0.30901699)462.53302
6generate(-0.5, -0.80901699, 0.30901699), (-0.809017, 0.30901699, -0.49999999), (0.309017, -0.50000001, -0.80901699)462.53302, 462.53302, 462.53302
7generate(1), (-1), (-1)462.53301, 462.53302
8generate(0.5, 0.80901699, 0.309017), (-0.80901699, 0.309017, 0.5), (0.309017, -0.5, 0.80901699)-142.93056, 231.26651, 88.33595
9generate(0.309017, 0.5, -0.80901699), (-0.5, 0.809017, 0.30901699), (0.80901699, 0.30901699, 0.5)231.26651, 88.33595, -142.93056
10generate(-0.30901699, -0.5, -0.809017), (-0.5, 0.80901699, -0.30901699), (0.809017, 0.30901699, -0.5)605.46358, 231.26651, 88.33595
11generate(0.30901699, 0.49999999, -0.809017), (0.50000001, -0.80901699, -0.309017), (-0.80901699, -0.30901699, -0.5)231.26651, 374.19707, 605.46358
12generate(-0.30901699, -0.5, -0.80901699), (0.5, -0.809017, 0.30901699), (-0.809017, -0.30901699, 0.5)605.46358, 231.26651, 374.19707
13generate(-0.5, -0.80901699, 0.309017), (0.80901699, -0.309017, 0.5), (-0.309017, 0.5, 0.80901699)462.53301
14generate(1), (1), (1)
15generate(0.5, 0.809017, 0.30901699), (0.809017, -0.309017, -0.5), (-0.309017, 0.5, -0.80901699)-142.93056, 231.26651, 374.19707
16generate(-0.80901699, 0.309017, 0.50000001), (0.30901699, -0.5, 0.80901699), (0.49999999, 0.809017, 0.30901699)231.2665, 88.33595, -142.93056
17generate(-0.5, 0.809017, 0.309017), (0.80901699, 0.309017, 0.5), (0.30901699, 0.5, -0.809017)88.33594, -142.93056, 231.26651
18generate(-0.5, 0.80901699, -0.309017), (0.80901699, 0.309017, -0.5), (-0.309017, -0.5, -0.80901699)231.26651, 88.33595, 605.46358
19generate(-0.809017, 0.30901699, -0.5), (0.309017, -0.5, -0.809017), (-0.5, -0.80901699, 0.309017)462.53302, 462.53302, 462.53302
20generate(-1), (-1), (1)462.53301, 462.53302
21generate(-1), (-1), (1)462.53302, 462.53302
22generate(-0.5, -0.80901699, -0.309017), (-0.809017, 0.30901699, 0.5), (-0.30901699, 0.5, -0.80901699)605.46358, 231.26651, 374.19707
23generate(-0.309017, -0.5, 0.80901699), (-0.5, 0.80901699, 0.309017), (-0.80901699, -0.309017, -0.5)231.26651, 88.33594, 605.46358
24generate(0.30901699, 0.5, 0.809017), (-0.5, 0.809017, -0.30901699), (-0.80901699, -0.30901699, 0.5)-142.93056, 231.26651, 374.19707
25generate(0.5, 0.80901699, -0.30901699), (-0.80901699, 0.309017, -0.5), (-0.30901699, 0.5, 0.809017)462.53302
26generate(-0.309017, 0.50000001, 0.80901699), (0.5, 0.80901699, -0.30901699), (-0.809017, 0.30901699, -0.49999999)462.53302
27generate(1), (-1), (-1)462.53302, 462.53302
28generate(-0.309017, 0.5, -0.80901699), (-0.5, -0.80901699, -0.309017), (-0.80901699, 0.309017, 0.5)374.19707, 605.46358, 231.26651
29generate(-0.80901699, -0.30901699, -0.5), (-0.309017, -0.5, 0.80901699), (-0.5, 0.809017, 0.30901699)605.46358, 231.26651, 88.33595
30generate(-0.809017, -0.30901699, 0.5), (0.30901699, 0.5, 0.809017), (-0.5, 0.80901699, -0.30901699)374.19707, -142.93056, 231.26651
31generate(0.80901699, 0.30901699, 0.5), (-0.30901699, -0.49999999, 0.809017), (0.50000001, -0.80901699, -0.309017)-142.93056, 231.26651, 374.19707
32generate(0.809017, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.809017, 0.30901699)88.33595, -142.93056, 231.26651
33generate(0.309017, -0.5, -0.80901699), (0.5, 0.80901699, -0.309017), (0.80901699, -0.309017, 0.5)462.53302
34generate(-1), (-1), (1)462.53302, 462.53302
35generate(0.309017, -0.5, 0.80901699), (-0.5, -0.809017, -0.30901699), (0.809017, -0.309017, -0.5)88.33595, 605.46358, 231.26651
36generate(-0.49999999, -0.809017, -0.30901699), (0.80901699, -0.309017, -0.50000001), (0.30901699, -0.5, 0.80901699)605.46358, 231.26651, 88.33595
37generate(-0.30901699, -0.5, 0.809017), (0.5, -0.809017, -0.309017), (0.80901699, 0.309017, 0.5)231.26651, 374.19707, -142.93056
38generate(0.309017, 0.5, 0.80901699), (0.5, -0.80901699, 0.309017), (0.80901699, 0.309017, -0.5)-142.93056, 231.26651, 88.33595
39generate(0.5, 0.80901699, -0.309017), (0.809017, -0.30901699, 0.5), (0.309017, -0.5, -0.809017)462.53302
40generate(-1), (1), (-1)462.53302, 462.53302
41generate(-1), (1), (-1)462.53302, 462.53302
42generate(0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.309017), (-0.809017, 0.30901699, 0.5)88.33594, -142.93056, 231.26651
43generate(0.80901699, 0.309017, 0.5), (0.309017, 0.5, -0.80901699), (-0.5, 0.80901699, 0.309017)-142.93056, 231.26651, 88.33595
44generate(0.80901699, 0.30901699, -0.5), (-0.30901699, -0.5, -0.809017), (-0.5, 0.809017, -0.30901699)88.33595, 605.46358, 231.26651
45generate(0.30901699, -0.5, -0.809017), (-0.5, -0.80901699, 0.30901699), (-0.80901699, 0.309017, -0.5)462.53302, 462.53302, 462.53302
46generate(0.809017, -0.30901699, 0.49999999), (0.309017, -0.50000001, -0.80901699), (0.5, 0.80901699, -0.30901699)462.53302
47generate(1), (-1), (-1)462.53302, 462.53302
48generate(0.80901699, -0.309017, -0.5), (0.309017, -0.5, 0.80901699), (-0.5, -0.80901699, -0.309017)231.26651, 88.33594, 605.46358
49generate(0.5, -0.809017, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.309017, -0.5, 0.80901699)374.19707, -142.93056, 231.26651
50generate(0.5, -0.80901699, 0.30901699), (0.809017, 0.30901699, -0.5), (0.30901699, 0.5, 0.809017)231.26651, 88.33595, -142.93056
51generate(-0.50000001, 0.80901699, 0.309017), (-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.49999999, 0.809017)88.33595, 605.46358, 231.26651
52generate(-0.5, 0.809017, -0.30901699), (-0.809017, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699)231.26651, 374.19707, -142.93056
53generate(-0.80901699, 0.309017, -0.5), (-0.309017, 0.5, 0.80901699), (0.5, 0.80901699, -0.309017)462.53302
54generate(-1), (1), (-1)462.53302, 462.53302
55generate(-0.809017, 0.309017, 0.5), (-0.309017, 0.5, -0.80901699), (-0.5, -0.809017, -0.30901699)231.26651, 374.19707, 605.46358
56generate(-0.30901699, 0.5, -0.80901699), (0.49999999, 0.809017, 0.30901699), (0.80901699, -0.309017, -0.50000001)374.19707, -142.93056, 231.26651
57generate(-0.80901699, -0.309017, -0.5), (0.30901699, 0.5, -0.809017), (0.5, -0.809017, -0.309017)605.46358, 231.26651, 374.19707
58generate(-0.80901699, -0.309017, 0.5), (-0.309017, -0.5, -0.80901699), (0.5, -0.80901699, 0.309017)374.19707, 605.46358, 231.26651
59generate(-0.309017, 0.5, 0.809017), (-0.5, -0.80901699, 0.309017), (0.809017, -0.30901699, 0.5)462.53302
60generate(1), (1), (1)

-
Components

#1: Protein Genome polyprotein


Mass: 33467.273 Da / Num. of mol.: 1 / Fragment: UNP residue 566-870 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / Cell line: Human rhabdomyosarcoma (RD) cell / Organ: homo sapiens, humanHuman / Strain: TW-2007-00141 / References: UniProt: A0A0K2BNC7
#2: Protein Genome polyprotein


Mass: 35638.730 Da / Num. of mol.: 1 / Fragment: UNP residues 1-325 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / Cell line: Human rhabdomyosarcoma (RD) cell / Organ: Homo sapiens, humanHuman / Strain: TW-2007-00141 / Tissue: muscleSkeletal muscle / References: UniProt: A0A0K2BNC7
#3: Protein Genome polyprotein


Mass: 26274.836 Da / Num. of mol.: 1 / Fragment: UNP residues 326-565 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / Cell line: human rhabdomyosarcoma (RD) cell / Organ: Homo sapiens, humanHuman / Tissue: muscleSkeletal muscle / References: UniProt: A0A0K2BNC7

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Coxsackievirus A6 / Type: VIRUS / Entity ID: all
Molecular weightExperimental value: NO
Source (natural)Organism: Coxsackievirus A6
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellName: Coxsackievirus A6 procapsid particle capsid / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Details: NaCl 137mmol/L, KCl 2.7mmol/L, Na2HPO4 10mmol/L, KH2PO4 2mmol/L
Buffer componentName: PBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 93000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1300 nm / Calibrated defocus max: 4000 nm / Cs: 2.3 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 312
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7

-
Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN2.1particle selection
2EPU1.4.3image acquisition
4CTFFIND4.1CTF correction
7Chimeramodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 30660
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10749 / Symmetry type: POINT
Atomic model buildingB value: 218.67 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0084940
ELECTRON MICROSCOPYf_angle_d0.8516751
ELECTRON MICROSCOPYf_dihedral_angle_d8.7923903
ELECTRON MICROSCOPYf_chiral_restr0.055752
ELECTRON MICROSCOPYf_plane_restr0.009862

+
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