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- PDB-4udf: STRUCTURAL BASIS OF HUMAN PARECHOVIRUS NEUTRALIZATION BY HUMAN MO... -

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Basic information

Entry
Database: PDB / ID: 4udf
TitleSTRUCTURAL BASIS OF HUMAN PARECHOVIRUS NEUTRALIZATION BY HUMAN MONOCLONAL ANTIBODIES
Components
  • (HUMAN MONOCLONAL ANTIBODY) x 2
  • Capsid protein VP0
  • Capsid protein VP3
KeywordsVIRUS / HUMAN PARECHOVIRUS 1 / HUMAN MONOCLONAL ANTIBODY / HPEV1-AM28 FAB
Function / homology
Function and homology information


host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain / LRAT domain profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain ...Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain / LRAT domain profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 / 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. / 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
Biological speciesHuman parechovirus 1
HOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 20 Å
AuthorsShakeel, S. / Westerhuis, B.M. / Ora, A. / Koen, G. / Bakker, A.Q. / Claassen, Y. / Beaumont, T. / Wolthers, K.C. / Butcher, S.J.
CitationJournal: J Virol / Year: 2015
Title: Structural Basis of Human Parechovirus Neutralization by Human Monoclonal Antibodies.
Authors: Shabih Shakeel / Brenda M Westerhuis / Ari Ora / Gerrit Koen / Arjen Q Bakker / Yvonne Claassen / Koen Wagner / Tim Beaumont / Katja C Wolthers / Sarah J Butcher /
Abstract: Since it was first recognized in 2004 that human parechoviruses (HPeV) are a significant cause of central nervous system and neonatal sepsis, their clinical importance, primarily in children, has ...Since it was first recognized in 2004 that human parechoviruses (HPeV) are a significant cause of central nervous system and neonatal sepsis, their clinical importance, primarily in children, has started to emerge. Intravenous immunoglobulin treatment is the only treatment available in such life-threatening cases and has given moderate success. Direct inhibition of parechovirus infection using monoclonal antibodies is a potential treatment. We have developed two neutralizing monoclonal antibodies against HPeV1 and HPeV2, namely, AM18 and AM28, which also cross-neutralize other viruses. Here, we present the mapping of their epitopes using peptide scanning, surface plasmon resonance, fluorescence-based thermal shift assays, electron cryomicroscopy, and image reconstruction. We determined by peptide scanning and surface plasmon resonance that AM18 recognizes a linear epitope motif including the arginine-glycine-aspartic acid on the C terminus of capsid protein VP1. This epitope is normally used by the virus to attach to host cell surface integrins during entry and is found in 3 other viruses that AM18 neutralizes. Therefore, AM18 is likely to cause virus neutralization by aggregation and by blocking integrin binding to the capsid. Further, we show by electron cryomicroscopy, three-dimensional reconstruction, and pseudoatomic model fitting that ordered RNA interacts with HPeV1 VP1 and VP3. AM28 recognizes quaternary epitopes on the capsid composed of VP0 and VP3 loops from neighboring pentamers, thereby increasing the RNA accessibility temperature for the virus-AM28 complex compared to the virus alone. Thus, inhibition of RNA uncoating probably contributes to neutralization by AM28.
IMPORTANCE: Human parechoviruses can cause mild infections to severe diseases in young children, such as neonatal sepsis, encephalitis, and cardiomyopathy. Intravenous immunoglobulin treatment is the ...IMPORTANCE: Human parechoviruses can cause mild infections to severe diseases in young children, such as neonatal sepsis, encephalitis, and cardiomyopathy. Intravenous immunoglobulin treatment is the only treatment available in such life-threatening cases. In order to develop more targeted treatment, we have searched for human monoclonal antibodies that would neutralize human parechoviruses 1 and 2, associated with mild infections such as gastroenteritis and severe infections of the central nervous system, and thus allow safe treatment. In the current study, we show how two such promising antibodies interact with the virus, modeling the atomic interactions between the virus and the antibody to propose how neutralization occurs. Both antibodies can cause aggregation; in addition, one antibody interferes with the virus recognizing its target cell, while the other, recognizing only the whole virus, inhibits the genome uncoating and replication in the cell.
History
DepositionDec 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references / Other
Revision 1.2Sep 16, 2015Group: Other
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Refinement description
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / em_3d_fitting / em_software / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _em_3d_fitting.target_criteria / _em_software.image_processing_id / _em_software.name
Revision 2.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title
Revision 2.2Oct 3, 2018Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
Revision 3.0Nov 6, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_nat / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion
Item: _atom_site.label_alt_id / _atom_sites.fract_transf_matrix[1][1] ..._atom_site.label_alt_id / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_nat.common_name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_polymer_linkage.label_alt_id_1

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Assembly

Deposited unit
1A: Capsid protein VP3
1B: Capsid protein VP0
1C: HUMAN MONOCLONAL ANTIBODY
1D: HUMAN MONOCLONAL ANTIBODY
1E: Capsid protein VP3
1F: Capsid protein VP0
1G: HUMAN MONOCLONAL ANTIBODY
1H: HUMAN MONOCLONAL ANTIBODY
1I: Capsid protein VP3
1J: Capsid protein VP0
1K: HUMAN MONOCLONAL ANTIBODY
1L: HUMAN MONOCLONAL ANTIBODY
1M: Capsid protein VP3
1N: Capsid protein VP0
1O: HUMAN MONOCLONAL ANTIBODY
1P: HUMAN MONOCLONAL ANTIBODY
1Q: Capsid protein VP3
1R: Capsid protein VP0
1S: HUMAN MONOCLONAL ANTIBODY
1T: HUMAN MONOCLONAL ANTIBODY
1U: Capsid protein VP3
1V: Capsid protein VP0
1W: HUMAN MONOCLONAL ANTIBODY
1X: HUMAN MONOCLONAL ANTIBODY
1Y: Capsid protein VP3
1Z: Capsid protein VP0
10: HUMAN MONOCLONAL ANTIBODY
11: HUMAN MONOCLONAL ANTIBODY
12: Capsid protein VP3
13: Capsid protein VP0
14: HUMAN MONOCLONAL ANTIBODY
15: HUMAN MONOCLONAL ANTIBODY
16: Capsid protein VP3
17: Capsid protein VP0
18: HUMAN MONOCLONAL ANTIBODY
19: HUMAN MONOCLONAL ANTIBODY
2A: Capsid protein VP3
2B: Capsid protein VP0
2C: HUMAN MONOCLONAL ANTIBODY
2D: HUMAN MONOCLONAL ANTIBODY
2E: Capsid protein VP3
2F: Capsid protein VP0
2G: HUMAN MONOCLONAL ANTIBODY
2H: HUMAN MONOCLONAL ANTIBODY
2I: Capsid protein VP3
2J: Capsid protein VP0
2K: HUMAN MONOCLONAL ANTIBODY
2L: HUMAN MONOCLONAL ANTIBODY
2M: Capsid protein VP3
2N: Capsid protein VP0
2O: HUMAN MONOCLONAL ANTIBODY
2P: HUMAN MONOCLONAL ANTIBODY
2Q: Capsid protein VP3
2R: Capsid protein VP0
2S: HUMAN MONOCLONAL ANTIBODY
2T: HUMAN MONOCLONAL ANTIBODY
2U: Capsid protein VP3
2V: Capsid protein VP0
2W: HUMAN MONOCLONAL ANTIBODY
2X: HUMAN MONOCLONAL ANTIBODY
2Y: Capsid protein VP3
2Z: Capsid protein VP0
20: HUMAN MONOCLONAL ANTIBODY
21: HUMAN MONOCLONAL ANTIBODY
22: Capsid protein VP3
23: Capsid protein VP0
24: HUMAN MONOCLONAL ANTIBODY
25: HUMAN MONOCLONAL ANTIBODY
26: Capsid protein VP3
27: Capsid protein VP0
28: HUMAN MONOCLONAL ANTIBODY
29: HUMAN MONOCLONAL ANTIBODY
3A: Capsid protein VP3
3B: Capsid protein VP0
3C: HUMAN MONOCLONAL ANTIBODY
3D: HUMAN MONOCLONAL ANTIBODY
3E: Capsid protein VP3
3F: Capsid protein VP0
3G: HUMAN MONOCLONAL ANTIBODY
3H: HUMAN MONOCLONAL ANTIBODY
3I: Capsid protein VP3
3J: Capsid protein VP0
3K: HUMAN MONOCLONAL ANTIBODY
3L: HUMAN MONOCLONAL ANTIBODY
3M: Capsid protein VP3
3N: Capsid protein VP0
3O: HUMAN MONOCLONAL ANTIBODY
3P: HUMAN MONOCLONAL ANTIBODY
3Q: Capsid protein VP3
3R: Capsid protein VP0
3S: HUMAN MONOCLONAL ANTIBODY
3T: HUMAN MONOCLONAL ANTIBODY
3U: Capsid protein VP3
3V: Capsid protein VP0
3W: HUMAN MONOCLONAL ANTIBODY
3X: HUMAN MONOCLONAL ANTIBODY
3Y: Capsid protein VP3
3Z: Capsid protein VP0
30: HUMAN MONOCLONAL ANTIBODY
31: HUMAN MONOCLONAL ANTIBODY
32: Capsid protein VP3
33: Capsid protein VP0
34: HUMAN MONOCLONAL ANTIBODY
35: HUMAN MONOCLONAL ANTIBODY
36: Capsid protein VP3
37: Capsid protein VP0
38: HUMAN MONOCLONAL ANTIBODY
39: HUMAN MONOCLONAL ANTIBODY
4A: Capsid protein VP3
4B: Capsid protein VP0
4C: HUMAN MONOCLONAL ANTIBODY
4D: HUMAN MONOCLONAL ANTIBODY
4E: Capsid protein VP3
4F: Capsid protein VP0
4G: HUMAN MONOCLONAL ANTIBODY
4H: HUMAN MONOCLONAL ANTIBODY
4I: Capsid protein VP3
4J: Capsid protein VP0
4K: HUMAN MONOCLONAL ANTIBODY
4L: HUMAN MONOCLONAL ANTIBODY
4M: Capsid protein VP3
4N: Capsid protein VP0
4O: HUMAN MONOCLONAL ANTIBODY
4P: HUMAN MONOCLONAL ANTIBODY
4Q: Capsid protein VP3
4R: Capsid protein VP0
4S: HUMAN MONOCLONAL ANTIBODY
4T: HUMAN MONOCLONAL ANTIBODY
4U: Capsid protein VP3
4V: Capsid protein VP0
4W: HUMAN MONOCLONAL ANTIBODY
4X: HUMAN MONOCLONAL ANTIBODY
4Y: Capsid protein VP3
4Z: Capsid protein VP0
40: HUMAN MONOCLONAL ANTIBODY
41: HUMAN MONOCLONAL ANTIBODY
42: Capsid protein VP3
43: Capsid protein VP0
44: HUMAN MONOCLONAL ANTIBODY
45: HUMAN MONOCLONAL ANTIBODY
46: Capsid protein VP3
47: Capsid protein VP0
48: HUMAN MONOCLONAL ANTIBODY
49: HUMAN MONOCLONAL ANTIBODY
5A: Capsid protein VP3
5B: Capsid protein VP0
5C: HUMAN MONOCLONAL ANTIBODY
5D: HUMAN MONOCLONAL ANTIBODY
5E: Capsid protein VP3
5F: Capsid protein VP0
5G: HUMAN MONOCLONAL ANTIBODY
5H: HUMAN MONOCLONAL ANTIBODY
5I: Capsid protein VP3
5J: Capsid protein VP0
5K: HUMAN MONOCLONAL ANTIBODY
5L: HUMAN MONOCLONAL ANTIBODY
5M: Capsid protein VP3
5N: Capsid protein VP0
5O: HUMAN MONOCLONAL ANTIBODY
5P: HUMAN MONOCLONAL ANTIBODY
5Q: Capsid protein VP3
5R: Capsid protein VP0
5S: HUMAN MONOCLONAL ANTIBODY
5T: HUMAN MONOCLONAL ANTIBODY
5U: Capsid protein VP3
5V: Capsid protein VP0
5W: HUMAN MONOCLONAL ANTIBODY
5X: HUMAN MONOCLONAL ANTIBODY
5Y: Capsid protein VP3
5Z: Capsid protein VP0
50: HUMAN MONOCLONAL ANTIBODY
51: HUMAN MONOCLONAL ANTIBODY
52: Capsid protein VP3
53: Capsid protein VP0
54: HUMAN MONOCLONAL ANTIBODY
55: HUMAN MONOCLONAL ANTIBODY
56: Capsid protein VP3
57: Capsid protein VP0
58: HUMAN MONOCLONAL ANTIBODY
59: HUMAN MONOCLONAL ANTIBODY
6A: Capsid protein VP3
6B: Capsid protein VP0
6C: HUMAN MONOCLONAL ANTIBODY
6D: HUMAN MONOCLONAL ANTIBODY
6E: Capsid protein VP3
6F: Capsid protein VP0
6G: HUMAN MONOCLONAL ANTIBODY
6H: HUMAN MONOCLONAL ANTIBODY
6I: Capsid protein VP3
6J: Capsid protein VP0
6K: HUMAN MONOCLONAL ANTIBODY
6L: HUMAN MONOCLONAL ANTIBODY
6M: Capsid protein VP3
6N: Capsid protein VP0
6O: HUMAN MONOCLONAL ANTIBODY
6P: HUMAN MONOCLONAL ANTIBODY
6Q: Capsid protein VP3
6R: Capsid protein VP0
6S: HUMAN MONOCLONAL ANTIBODY
6T: HUMAN MONOCLONAL ANTIBODY
6U: Capsid protein VP3
6V: Capsid protein VP0
6W: HUMAN MONOCLONAL ANTIBODY
6X: HUMAN MONOCLONAL ANTIBODY
6Y: Capsid protein VP3
6Z: Capsid protein VP0
60: HUMAN MONOCLONAL ANTIBODY
61: HUMAN MONOCLONAL ANTIBODY
62: Capsid protein VP3
63: Capsid protein VP0
64: HUMAN MONOCLONAL ANTIBODY
65: HUMAN MONOCLONAL ANTIBODY
66: Capsid protein VP3
67: Capsid protein VP0
68: HUMAN MONOCLONAL ANTIBODY
69: HUMAN MONOCLONAL ANTIBODY
7A: Capsid protein VP3
7B: Capsid protein VP0
7C: HUMAN MONOCLONAL ANTIBODY
7D: HUMAN MONOCLONAL ANTIBODY
7E: Capsid protein VP3
7F: Capsid protein VP0
7G: HUMAN MONOCLONAL ANTIBODY
7H: HUMAN MONOCLONAL ANTIBODY
7I: Capsid protein VP3
7J: Capsid protein VP0
7K: HUMAN MONOCLONAL ANTIBODY
7L: HUMAN MONOCLONAL ANTIBODY
7M: Capsid protein VP3
7N: Capsid protein VP0
7O: HUMAN MONOCLONAL ANTIBODY
7P: HUMAN MONOCLONAL ANTIBODY
7Q: Capsid protein VP3
7R: Capsid protein VP0
7S: HUMAN MONOCLONAL ANTIBODY
7T: HUMAN MONOCLONAL ANTIBODY
7U: Capsid protein VP3
7V: Capsid protein VP0
7W: HUMAN MONOCLONAL ANTIBODY
7X: HUMAN MONOCLONAL ANTIBODY


Theoretical massNumber of molelcules
Total (without water)4,281,020240
Polymers4,281,020240
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Capsid protein VP3 / P1C / Virion protein 3


Mass: 20555.203 Da / Num. of mol.: 60 / Fragment: UNP residues 360-542 / Source method: isolated from a natural source
Details: FAB FRAGMENTS OF HUMAN MONOCLONAL ANTIBODY, AM28 WERE ATTACHED TO THE VIRUS
Source: (natural) Human parechovirus 1 (strain Harris) / Strain: Harris / References: UniProt: Q66578
#2: Protein ...
Capsid protein VP0 / P1AB / Virion protein 0


Mass: 25594.449 Da / Num. of mol.: 60 / Fragment: UNP residues 61-289 / Source method: isolated from a natural source
Details: FAB FRAGMENTS OF HUMAN MONOCLONAL ANTIBODY, AM28 WERE ATTACHED TO THE VIRUS
Source: (natural) Human parechovirus 1 (strain Harris) / Strain: Harris / References: UniProt: Q66578
#3: Antibody ...
HUMAN MONOCLONAL ANTIBODY


Mass: 12168.451 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#4: Antibody ...
HUMAN MONOCLONAL ANTIBODY


Mass: 13032.227 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: AM28 FAB FRAGMENT IN COMPLEX WITH HUMAN PARECHOVIRUS 1
Type: VIRUS
Details of virusHost category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 10mM TRIS HCl, 150 mM NaCl, 1mM MgCl2 (1X TNM Buffer) / pH: 7.5
Details: 10mM TRIS HCl, 150 mM NaCl, 1mM MgCl2 (1X TNM Buffer)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Feb 1, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 69000 X / Nominal defocus max: 4060 nm / Nominal defocus min: 1650 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC GATAN
Image scansNum. digital images: 65

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Processing

EM softwareName: Auto3DEM / Category: 3D reconstruction
CTF correctionDetails: WHOLE MICROGRAPH
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: POLAR FOURIER TRANSFORM / Resolution: 20 Å / Num. of particles: 270 / Nominal pixel size: 2.17 Å
Magnification calibration: SYMMETRY RELATED VP0 HELICES FITTING IN EM DENSITY
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2761
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--MOLECULAR DYNAMIC SIMULATION AND NORMAL MODE ANALYSIS REFINEMENT PROTOCOL--HOMOLOGY MODEL
RefinementHighest resolution: 20 Å

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