[English] 日本語
Yorodumi
- PDB-2hwc: A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hwc
TitleA COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A
Components
  • HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)
  • HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)
  • HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)
  • HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)
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-W54 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 14
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsKim, K.H. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A.
Authors: Kim, K.H. / Willingmann, P. / Gong, Z.X. / Kremer, M.J. / Chapman, M.S. / Minor, I. / Oliveira, M.A. / Rossmann, M.G. / Andries, K. / Diana, G.D. / Dutko, F.J. / McKinlay, M.A. / Pevear, D.C.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Human Rhinovirus 14 Complexed with Antiviral Compound R 61837
Authors: Chapman, M.S. / Minor, I. / Rossmann, M.G. / Diana, G.D. / Andries, K.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)
Authors: Kim, S. / Smith, T.J. / Chapman, M.S. / Rossmann, M.G. / Pevear, D.C. / Dutko, F.J. / Felock, P.J. / Diana, G.D. / Mckinlay, M.A.
#3: Journal: Biochemistry / 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.
#4: 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.
#5: 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.
History
DepositionJan 25, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / 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_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.auth_atom_id_1 / _pdbx_validate_rmsd_bond.auth_atom_id_2 / _pdbx_validate_rmsd_bond.auth_comp_id_1 / _pdbx_validate_rmsd_bond.auth_comp_id_2 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_standard_deviation / _pdbx_validate_rmsd_bond.bond_target_value / _pdbx_validate_rmsd_bond.bond_value / _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 29, 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)94,8525
Polymers94,4694
Non-polymers3831
Water00
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)5,691,106300
Polymers5,668,110240
Non-polymers22,99660
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
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)474,25925
Polymers472,34320
Non-polymers1,9165
Water0
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)569,11130
Polymers566,81124
Non-polymers2,3006
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
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)1,897,035100
Polymers1,889,37080
Non-polymers7,66520
Water0
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: CIS PROLINE - PRO 2 83
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

#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 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303
#2: Protein HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)


Mass: 28487.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / 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 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / 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 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303
#5: Chemical ChemComp-W54 / 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLY)PHENOXY)PENTYL)-3-METHYL ISOXAZOLE / WIN54954


Mass: 383.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20Cl2N2O3
Nonpolymer detailsWIN54954 IS 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2- OXAZOLYL)PHENOXY)PENTYL)-3-METHYL ISOXAZOLE.
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: POLG_HRV14 SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ILE 170 VAL 2 170 THE ABOVE DISCREPANCY IS DUE TO A SPONTANEOUS MUTATION WHICH OCCURRED IN THE VIRUS STOCK.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlvirus1drop
20.25 %(w/v)PEG80001dropor 0.5 %(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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 352588 / Redundancy: 11.1 % / Rmerge(I) obs: 0.111

-
Processing

RefinementHighest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6267 0 25 0 6292

+
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