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- PDB-3eti: Structure of a cubic crystal form of X (ADRP) domain from FCoV -

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Entry
Database: PDB / ID: 3eti
TitleStructure of a cubic crystal form of X (ADRP) domain from FCoV
Componentsmacro domain of Non-structural protein 3
KeywordsRNA BINDING PROTEIN / coronavirus / macro / ADRP / X domain
Function / homology
Function and homology information


host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 ...host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / : / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain ...Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / : / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Coronavirus 3Ecto domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesFeline infectious peritonitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWojdyla, J.A. / Manolaridis, I. / Tucker, P.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the X (ADRP) domain of nsp3 from feline coronavirus
Authors: Wojdyla, J.A. / Manolaridis, I. / Snijder, E.J. / Gorbalenya, A.E. / Coutard, B. / Piotrowski, Y. / Hilgenfeld, R. / Tucker, P.A.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Dec 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: macro domain of Non-structural protein 3
B: macro domain of Non-structural protein 3
C: macro domain of Non-structural protein 3
D: macro domain of Non-structural protein 3
E: macro domain of Non-structural protein 3
F: macro domain of Non-structural protein 3
G: macro domain of Non-structural protein 3
H: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)147,6598
Polymers147,6598
Non-polymers00
Water42,2092343
1
A: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4571
Polymers18,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4571
Polymers18,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4571
Polymers18,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4571
Polymers18,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4571
Polymers18,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4571
Polymers18,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4571
Polymers18,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4571
Polymers18,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)218.990, 218.990, 218.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11H-426-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALAAA35 - 682 - 35
21LEULEUALAALABB35 - 682 - 35
31LEULEUALAALACC35 - 682 - 35
41LEULEUALAALADD35 - 682 - 35
51LEULEUALAALAEE35 - 682 - 35
61LEULEUALAALAFF35 - 682 - 35
71LEULEUALAALAGG35 - 682 - 35
81LEULEUALAALAHH35 - 682 - 35
12HISHISALAALAAA74 - 7941 - 46
22HISHISALAALABB74 - 7941 - 46
32HISHISALAALACC74 - 7941 - 46
42HISHISALAALADD74 - 7941 - 46
52HISHISALAALAEE74 - 7941 - 46
62HISHISALAALAFF74 - 7941 - 46
72HISHISALAALAGG74 - 7941 - 46
82HISHISALAALAHH74 - 7941 - 46
13ALAALATHRTHRAA81 - 9148 - 58
23ALAALATHRTHRBB81 - 9148 - 58
33ALAALATHRTHRCC81 - 9148 - 58
43ALAALATHRTHRDD81 - 9148 - 58
53ALAALATHRTHREE81 - 9148 - 58
63ALAALATHRTHRFF81 - 9148 - 58
73ALAALATHRTHRGG81 - 9148 - 58
83ALAALATHRTHRHH81 - 9148 - 58
14GLUGLUPHEPHEAA96 - 11263 - 79
24GLUGLUPHEPHEBB96 - 11263 - 79
34GLUGLUPHEPHECC96 - 11263 - 79
44GLUGLUPHEPHEDD96 - 11263 - 79
54GLUGLUPHEPHEEE96 - 11263 - 79
64GLUGLUPHEPHEFF96 - 11263 - 79
74GLUGLUPHEPHEGG96 - 11263 - 79
84GLUGLUPHEPHEHH96 - 11263 - 79
15ASNASNSERSERAA114 - 13281 - 99
25ASNASNSERSERBB114 - 13281 - 99
35ASNASNSERSERCC114 - 13281 - 99
45ASNASNSERSERDD114 - 13281 - 99
55ASNASNSERSEREE114 - 13281 - 99
65ASNASNSERSERFF114 - 13281 - 99
75ASNASNSERSERGG114 - 13281 - 99
85ASNASNSERSERHH114 - 13281 - 99
16GLYGLYCYSCYSAA136 - 139103 - 106
26GLYGLYCYSCYSBB136 - 139103 - 106
36GLYGLYCYSCYSCC136 - 139103 - 106
46GLYGLYCYSCYSDD136 - 139103 - 106
56GLYGLYCYSCYSEE136 - 139103 - 106
66GLYGLYCYSCYSFF136 - 139103 - 106
76GLYGLYCYSCYSGG136 - 139103 - 106
86GLYGLYCYSCYSHH136 - 139103 - 106
17VALVALLEULEUAA141 - 166108 - 133
27VALVALLEULEUBB141 - 166108 - 133
37VALVALLEULEUCC141 - 166108 - 133
47VALVALLEULEUDD141 - 166108 - 133
57VALVALLEULEUEE141 - 166108 - 133
67VALVALLEULEUFF141 - 166108 - 133
77VALVALLEULEUGG141 - 166108 - 133
87VALVALLEULEUHH141 - 166108 - 133
18VALVALLEULEUAA168 - 170135 - 137
28VALVALLEULEUBB168 - 170135 - 137
38VALVALLEULEUCC168 - 170135 - 137
48VALVALLEULEUDD168 - 170135 - 137
58VALVALLEULEUEE168 - 170135 - 137
68VALVALLEULEUFF168 - 170135 - 137
78VALVALLEULEUGG168 - 170135 - 137
88VALVALLEULEUHH168 - 170135 - 137
19CYSCYSTHRTHRAA172 - 188139 - 155
29CYSCYSTHRTHRBB172 - 188139 - 155
39CYSCYSTHRTHRCC172 - 188139 - 155
49CYSCYSTHRTHRDD172 - 188139 - 155
59CYSCYSTHRTHREE172 - 188139 - 155
69CYSCYSTHRTHRFF172 - 188139 - 155
79CYSCYSTHRTHRGG172 - 188139 - 155
89CYSCYSTHRTHRHH172 - 188139 - 155
110VALVALGLUGLUAA193 - 196160 - 163
210VALVALGLUGLUBB193 - 196160 - 163
310VALVALGLUGLUCC193 - 196160 - 163
410VALVALGLUGLUDD193 - 196160 - 163
510VALVALGLUGLUEE193 - 196160 - 163
610VALVALGLUGLUFF193 - 196160 - 163
710VALVALGLUGLUGG193 - 196160 - 163
810VALVALGLUGLUHH193 - 196160 - 163

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Components

#1: Protein
macro domain of Non-structural protein 3 / X (ADRP) domain


Mass: 18457.342 Da / Num. of mol.: 8 / Mutation: L122M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline infectious peritonitis virus / Strain: FIPV WSU-79/1146 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLys / References: UniProt: Q98VG9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2343 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.926919 Å3/Da / Density % sol: 79.247231 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2008
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 176415 / Num. obs: 176075 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 21.5 % / Biso Wilson estimate: 31.389 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 20.33
Reflection shellResolution: 2.2→2.33 Å / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 5.6 / Num. measured obs: 605300 / Num. unique obs: 28013 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.17 / WRfactor Rwork: 0.139 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.915 / SU B: 2.869 / SU ML: 0.074 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.181 8797 5 %RANDOM
Rwork0.147 ---
obs0.149 175890 99.99 %-
all-175890 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 88.69 Å2 / Biso mean: 39.885 Å2 / Biso min: 7.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10668 0 0 2343 13011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02210882
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.97614775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37751428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24324.754488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.095151983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3821564
X-RAY DIFFRACTIONr_chiral_restr0.1120.21726
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218124
X-RAY DIFFRACTIONr_mcbond_it0.9061.56787
X-RAY DIFFRACTIONr_mcangle_it1.661211003
X-RAY DIFFRACTIONr_scbond_it2.81434095
X-RAY DIFFRACTIONr_scangle_it4.6784.53729
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A564MEDIUM POSITIONAL0.10.5
B564MEDIUM POSITIONAL0.140.5
C564MEDIUM POSITIONAL0.080.5
D564MEDIUM POSITIONAL0.080.5
E564MEDIUM POSITIONAL0.120.5
F564MEDIUM POSITIONAL0.110.5
G564MEDIUM POSITIONAL0.110.5
H564MEDIUM POSITIONAL0.110.5
A500LOOSE POSITIONAL0.365
B500LOOSE POSITIONAL0.385
C500LOOSE POSITIONAL0.355
D500LOOSE POSITIONAL0.355
E500LOOSE POSITIONAL0.335
F500LOOSE POSITIONAL0.385
G500LOOSE POSITIONAL0.35
H500LOOSE POSITIONAL0.375
A564MEDIUM THERMAL1.652
B564MEDIUM THERMAL0.942
C564MEDIUM THERMAL0.752
D564MEDIUM THERMAL0.752
E564MEDIUM THERMAL1.382
F564MEDIUM THERMAL3.152
G564MEDIUM THERMAL1.822
H564MEDIUM THERMAL1.822
A500LOOSE THERMAL1.56
B500LOOSE THERMAL1.12
C500LOOSE THERMAL0.78
D500LOOSE THERMAL0.78
E500LOOSE THERMAL1.57
F500LOOSE THERMAL2.74
G500LOOSE THERMAL1.66
H500LOOSE THERMAL1.78
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 599 -
Rwork0.174 12262 -
all-12861 -
obs--99.87 %

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