[English] 日本語
Yorodumi
- PDB-2rs1: STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rs1
TitleSTRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES
Components(HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT ...) x 4
KeywordsVIRUS / RHINOVIRUS COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into host cell / 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 / nucleoside-triphosphate phosphatase / channel activity ...lysis of host organelle involved in viral entry into host cell / 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / 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 / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 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 coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 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 / Few Secondary Structures / Irregular / 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
Chem-W84 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus sp.
Human rhinovirus
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsBadger, J. / Smith, T.J. / Rossmann, M.G.
Citation
Journal: Proteins / Year: 1989
Title: Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.
Authors: Badger, J. / Minor, I. / Oliveira, M.A. / Smith, T.J. / Rossmann, M.G.
#1: Journal: To be Published
Title: The Use of Molecular Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure
Authors: Arnold, E. / Rossmann, M.G.
#2: Journal: To be Published
Title: Analysis of the Structure of a Common Cold Virus, Human Rhinovirus 14, Refined at a Resolution of 3.0 Angstroms
Authors: Arnold, E. / Rossmann, M.G.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Three-Dimensional Structures of Drug-Resistant Mutants of Human Rhinovirus 14
Authors: Badger, J. / Krishnaswamy, S. / Kremer, M.J. / Oliveira, M.A. / Rossmann, M.G. / Heinz, B.A. / Rueckert, R.R. / Dutko, F.J. / Mckinlay, M.A.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14
Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F. ...Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F.J. / Fancher, M. / Rueckert, R.R. / Heinz, B.A.
#5: Journal: Acta Crystallogr.,Sect.A / Year: 1987
Title: The Structure Determination of a Common Cold Virus, Human Rhinovirus 14
Authors: Arnold, E. / Vriend, G. / Luo, M. / Griffith, J.P. / Kamer, G. / Erickson, J.W. / Johnson, J.E. / Rossmann, M.G.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Implications of the Picornavirus Capsid Structure for Polyprotein Structure
Authors: Arnold, E. / Luo, M. / Vriend, G. / Rossmann, M.G. / Palmenberg, A.C. / Parks, G.D. / Nicklin, M.J.H. / Wimmer, E.
#7: Journal: Science / Year: 1986
Title: The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
Authors: Smith, T.J. / Kremer, M.J. / Luo, M. / Vriend, G. / Arnold, E. / Kamer, G. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Otto, M.J.
#8: Journal: Chem.Scr. / Year: 1987
Title: The Structure of a Human Common Cold Virus (Rhinovirus 14) and its Evolutionary Relations to Other Viruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Vriend, G.
#9: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G.
#10: Journal: J.Mol.Biol. / Year: 1984
Title: Virion Orientation in Cubic Crystals of the Human Common Cold Virus Hrv14
Authors: Arnold, E. / Erickson, J.W. / Fout, G.S. / Frankenberger, E.A. / Hecht, H.-J. / Luo, M. / Rossmann, M.G. / Rueckert, R.R.
#11: Journal: J.Mol.Biol. / Year: 1984
Title: Picornaviruses of Two Different Genera Have Similar Structures
Authors: Luo, M. / Arnold, E. / Erickson, J.W. / Rossmann, M.G. / Boege, U. / Scraba, D.G.
#12: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983
Title: Crystallization of a Common Cold Virus, Human Rhinovirus 14. (Quote)Isomorphism(Quote) with Poliovirus Crystals
Authors: Erickson, J.W. / Frankenberger, E.A. / Rossmann, M.G. / Fout, G.S. / Medappa, K.C. / Rueckert, R.R.
History
DepositionOct 3, 1988Processing site: BNL
SupersessionJan 15, 1990ID: 1RS1
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jan 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / diffrn / pdbx_database_remark / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE ...SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE REDUNDANT SHEETS ARE DEFINED. THUS SHEETS B11 AND B12 DIFFER ONLY IN STRAND 4, SHEETS B12 AND B22 DIFFER ONLY IN STRAND 4, AND SHEETS B13 AND B23 DIFFER IN STRANDS 1 AND 4 (DOUBLY BIFURCATED).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8395
Polymers94,4834
Non-polymers3561
Water1448
1
1: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,690,339300
Polymers5,668,952240
Non-polymers21,38860
Water2,162120
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
1: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)474,19525
Polymers472,41320
Non-polymers1,7825
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)569,03430
Polymers566,89524
Non-polymers2,1396
Water21612
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
1: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.9 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,896,780100
Polymers1,889,65180
Non-polymers7,12920
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)445.100, 445.100, 445.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Atom site foot note1: RESIDUE PRO 2 83 IS A CIS PROLINE.
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.46428249, -0.82990465, 0.30935523), (0.84439659, 0.30935523, -0.43737202), (0.26727602, 0.46428249, 0.84439659)0.18336, 0.04923, -0.09998
3generate(-0.40252706, -0.49841714, 0.7678235), (0.53635794, -0.80813188, -0.2434001), (0.74181712, 0.31385302, 0.5926246)0.1967, 0.26302, -0.11254
4generate(-0.40252706, 0.53635794, 0.74181712), (-0.49841714, -0.80813188, 0.31385302), (0.7678235, -0.2434001, 0.5926246)0.02159, 0.34591, -0.02032
5generate(0.46428249, 0.84439659, 0.26727602), (-0.82990465, 0.30935523, 0.46428249), (0.30935523, -0.43737202, 0.84439659)-0.09998, 0.18336, 0.04923
6generate(-0.6305654, -0.70150875, 0.33207415), (-0.70150875, 0.33207415, -0.6305654), (0.33207415, -0.6305654, -0.70150875)0.34718, 0.34718, 0.34718
7generate(-0.79635651, 0.46046981, 0.39215364), (-0.21383107, 0.39215364, -0.89470238), (-0.56576752, -0.79635651, -0.21383107)0.16382, 0.29795, 0.44716
8generate(0.12389799, 0.98541842, -0.11662042), (-0.00727745, -0.11662042, -0.99315013), (-0.99226854, 0.12389799, -0.00727745)0.00127, 0.3675, 0.32559
9generate(0.85843766, 0.14787594, -0.49113956), (-0.36729797, -0.49113956, -0.7898572), (-0.35801899, 0.85843766, -0.36729797)0.08416, 0.45972, 0.15048
10generate(0.39215364, -0.89470238, -0.21383107), (-0.79635651, -0.21383107, -0.56576752), (0.46046981, 0.39215364, -0.79635651)0.29795, 0.44716, 0.16382
11generate(-0.49113956, -0.7898572, -0.36729797), (0.85843766, -0.36729797, -0.35801899), (0.14787594, -0.49113956, 0.85843766)0.45972, 0.15048, 0.08416
12generate(-0.99315013, -0.00727745, -0.11662042), (-0.00727745, -0.99226854, 0.12389799), (-0.11662042, 0.12389799, 0.98541842)0.3675, 0.32559, 0.00127
13generate(-0.49841714, 0.7678235, -0.40252706), (-0.80813188, -0.2434001, 0.53635794), (0.31385302, 0.5926246, 0.74181712)0.1967, 0.26302, -0.11254
14generate(0.30935523, 0.46428249, -0.82990465), (-0.43737202, 0.84439659, 0.30935523), (0.84439659, 0.26727602, 0.46428249)0.18336, 0.04923, -0.09998
15generate(0.31385302, -0.49841714, -0.80813188), (0.5926246, 0.7678235, -0.2434001), (0.74181712, -0.40252706, 0.53635794)0.34591, -0.02032, 0.02159
16generate(-0.2434001, 0.5926246, 0.7678235), (0.53635794, 0.74181712, -0.40252706), (-0.80813188, 0.31385302, -0.49841714)-0.02032, 0.02159, 0.34591
17generate(0.5926246, 0.74181712, 0.31385302), (0.7678235, -0.40252706, -0.49841714), (-0.2434001, 0.53635794, -0.80813188)-0.11254, 0.1967, 0.26302
18generate(0.98541842, -0.11662042, 0.12389799), (-0.11662042, -0.99315013, -0.00727745), (0.12389799, -0.00727745, -0.99226854)0.00127, 0.3675, 0.32559
19generate(0.39215364, -0.79635651, 0.46046981), (-0.89470238, -0.21383107, 0.39215364), (-0.21383107, -0.56576752, -0.79635651)0.16382, 0.29795, 0.44716
20generate(-0.36729797, -0.35801899, 0.85843766), (-0.49113956, 0.85843766, 0.14787594), (-0.7898572, -0.36729797, -0.49113956)0.15048, 0.08416, 0.45972

-
Components

-
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT ... , 4 types, 4 molecules 1234

#1: Protein HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)


Mass: 32560.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: 14 / References: UniProt: P03303
#2: Protein HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)


Mass: 28501.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: 14 / References: UniProt: P03303
#3: Protein HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)


Mass: 26236.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus / Genus: Rhinovirus / Species: Human rhinovirus B / Strain: 14 / References: UniProt: P03303
#4: Protein HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)


Mass: 7183.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: 14 / References: UniProt: P03303

-
Non-polymers , 2 types, 9 molecules

#5: Chemical ChemComp-W84 / 5-(7-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE / WIN I(S) / WIN 52084 (S)


Mass: 356.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop / Details: Arnold, E., (1984) J.Mol.Biol., 177, 417.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlvirus1drop
20.125 %(w/v)PEG80001dropor 0.25%(w/v)
30.01 M1dropCaCl2
40.01 MTris-HCl1drop
50.25 %(w/v)PEG80001reservoiror 0.5%(w/v)
60.02 M1reservoirCaCl2
70.01 MTris-HCl1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 335902 / Observed criterion σ(I): 1 / Num. measured all: 591945 / Rmerge(I) obs: 0.11

-
Processing

SoftwareName: REAL-SPACE / Version: REFINEMENT / Classification: refinement
RefinementHighest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 26 8 6302
Refinement
*PLUS
Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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