[English] 日本語
Yorodumi
- PDB-8p24: The crystal structure of the C-terminal domain of Mengla nucleoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p24
TitleThe crystal structure of the C-terminal domain of Mengla nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Nucleoprotein / Filovirus / Mengla
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / Nucleoprotein
Function and homology information
Biological speciesMengla dianlovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.73 Å
AuthorsFerrero, D.S. / Tomas Gilabert, O. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117976GB-I00 Spain
CitationJournal: Microbiol Spectr / Year: 2023
Title: Structural insights on the nucleoprotein C-terminal domain of Mengla virus.
Authors: Ferrero, D.S. / Tomas Gilabert, O. / Verdaguer, N.
History
DepositionMay 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
V: Nucleoprotein
Z: Nucleoprotein
Y: Nucleoprotein
T: Nucleoprotein
P: Nucleoprotein
S: Nucleoprotein
X: Nucleoprotein
W: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein
U: Nucleoprotein
a: Nucleoprotein
O: Nucleoprotein
A: Nucleoprotein
E: Nucleoprotein
L: Nucleoprotein
K: Nucleoprotein
H: Nucleoprotein
B: Nucleoprotein
G: Nucleoprotein
C: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
I: Nucleoprotein
D: Nucleoprotein
J: Nucleoprotein
F: Nucleoprotein
b: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)399,77128
Polymers399,77128
Non-polymers00
Water00
1
V: Nucleoprotein
Z: Nucleoprotein
Y: Nucleoprotein
T: Nucleoprotein
P: Nucleoprotein
S: Nucleoprotein
X: Nucleoprotein
W: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein
U: Nucleoprotein
a: Nucleoprotein
O: Nucleoprotein
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)199,88614
Polymers199,88614
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Nucleoprotein
L: Nucleoprotein
K: Nucleoprotein
H: Nucleoprotein
B: Nucleoprotein
G: Nucleoprotein
C: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
I: Nucleoprotein
D: Nucleoprotein
J: Nucleoprotein
F: Nucleoprotein
b: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)199,88614
Polymers199,88614
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.748, 162.942, 175.363
Angle α, β, γ (deg.)90.000, 99.151, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "a" and (resid 638 or resid 640 or resid...
d_2ens_1(chain "b" and (resid 638 or resid 640 or resid...
d_3ens_1(chain "A" and (resid 638 or resid 640 or resid...
d_4ens_1(chain "B" and (resid 638 or resid 640 or resid...
d_5ens_1(chain "C" and (resid 638 or resid 640 or resid...
d_6ens_1(chain "D" and (resid 638 or resid 640 or resid...
d_7ens_1(chain "E" and (resid 638 or resid 640 or resid...
d_8ens_1(chain "F" and (resid 638 or resid 640 or resid...
d_9ens_1(chain "G" and (resid 638 or resid 640 or resid...
d_10ens_1(chain "H" and (resid 638 or resid 640 or resid...
d_11ens_1(chain "I" and (resid 638 or resid 640 or resid...
d_12ens_1(chain "J" and (resid 638 or resid 640 or resid...
d_13ens_1(chain "K" and (resid 638 or resid 640 or resid...
d_14ens_1(chain "L" and (resid 638 or resid 640 or resid...
d_15ens_1(chain "M" and (resid 638 or resid 640 or resid...
d_16ens_1(chain "N" and (resid 638 or resid 640 or resid...
d_17ens_1(chain "O" and (resid 638 or resid 640 or resid...
d_18ens_1(chain "P" and (resid 638 or resid 640 or resid...
d_19ens_1(chain "Q" and (resid 638 or resid 640 or resid...
d_20ens_1(chain "R" and (resid 638 or resid 640 or resid...
d_21ens_1(chain "S" and (resid 638 or resid 640 or resid...
d_22ens_1(chain "T" and (resid 638 or resid 640 or resid...
d_23ens_1(chain "U" and (resid 638 or resid 640 or resid...
d_24ens_1(chain "V" and (resid 638 or resid 640 or resid...
d_25ens_1(chain "W" and (resid 638 or resid 640 or resid...
d_26ens_1(chain "X" and (resid 638 or resid 640 or resid...
d_27ens_1(chain "Y" and (resid 638 or resid 640 or resid...
d_28ens_1(chain "Z" and (resid 638 or resid 640 or resid...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1GLNGLNVA632 - 69765 - 130
d_2ASPASPZB633 - 69766 - 130
d_3ASPASPYC633 - 69766 - 130
d_4TRPTRPTD634 - 69767 - 130
d_5ARGARGPE636 - 69769 - 130
d_6ARGARGSF636 - 69769 - 130
d_7GLNGLNXG632 - 69765 - 130
d_8PROPROWH635 - 69768 - 130
d_9ASPASPQI633 - 69766 - 130
d_10PROPRORJ635 - 69768 - 130
d_11TRPTRPUK634 - 69767 - 130
d_12TRPTRPaL634 - 69767 - 130
d_13ASPASPOM633 - 69766 - 130
d_14GLNGLNAN632 - 69765 - 130
d_15ASPASPEO633 - 69766 - 130
d_16TRPTRPLP634 - 69767 - 130
d_17GLNGLNKQ632 - 69765 - 130
d_18PROPROHR635 - 69768 - 130
d_19TRPTRPBS634 - 69767 - 130
d_20ARGARGGT636 - 69769 - 130
d_21TRPTRPCU634 - 69767 - 130
d_22SERSERMV631 - 69764 - 130
d_23GLNGLNNW632 - 69765 - 130
d_24ASPASPIX633 - 69766 - 130
d_25TRPTRPDY634 - 69767 - 130
d_26GLNGLNJZ632 - 69765 - 130
d_27TRPTRPFAA634 - 69767 - 130
d_28TRPTRPbBA634 - 69767 - 130

NCS oper:
IDCodeMatrixVector
1given(0.856297837092, -0.400914710046, -0.325609289579), (0.406104138872, 0.912161919794, -0.0551367433715), (0.319113526167, -0.0850178060601, 0.943895402081)-3.88783526873, 44.9186778444, -37.8646651343
2given(-0.558820586456, -0.757144393263, 0.338307434005), (0.768580052227, -0.626068916016, -0.131614648566), (0.311455061721, 0.186467370199, 0.931786276127)-2.85406308207, 62.561828277, -166.831540741
3given(0.165209533435, 0.970119883543, -0.177688552297), (-0.939725301558, 0.209526040806, 0.270213241414), (0.299369617151, 0.122336624849, 0.946261899554)-62.2098061629, 66.3147976474, -21.0699627906
4given(-0.905984723614, -0.422857320736, 0.0195797568343), (0.422406181041, -0.906103509909, -0.0234402975464), (0.0276531878085, -0.0129659411839, 0.999533483968)-8.03442312858, 112.908443909, -28.7986724863
5given(0.588976180225, -0.751381156992, -0.297545653714), (0.767547047011, 0.635325757847, -0.0850453528414), (0.252939893555, -0.178290600797, 0.950912126285)4.67077529725, 55.7811554231, 3.37995601827
6given(-0.2142859295, 0.974949745215, -0.0596199188433), (-0.953859046778, -0.19572654223, 0.227692862309), (0.210319897532, 0.105660375597, 0.971906078657)-60.9012831517, 83.3219645298, -58.5422162012
7given(-0.65215791791, -0.757870686859, 0.017946367525), (0.749260493358, -0.647988606178, -0.136819148351), (0.115320263615, -0.075781186733, 0.990433464972)6.5895854156, 105.809426074, -63.9672679181
8given(0.952558869301, -0.00640956567671, -0.304286900775), (-4.48169700804E-5, 0.999775258361, -0.0211997820686), (0.304354396234, 0.0202076776537, 0.952344502403)-17.0895308531, 43.5826172581, -79.6274264672
9given(-0.627677196104, 0.776566854104, -0.0544541880657), (-0.777267384664, -0.62127676298, 0.0993508757822), (0.0433214753665, 0.104685743483, 0.993561344298)-44.2438036751, 106.43173119, -94.6320723905
10given(-0.231017736195, -0.964415886135, -0.128579952304), (0.953606415554, -0.198218092081, -0.226593010011), (0.193043025716, -0.174961671639, 0.965465071186)24.2388142084, 93.6780592219, -96.8724696919
11given(0.832245255136, 0.443613487047, -0.332528058085), (-0.466190808939, 0.884583962252, 0.0133170336905), (0.300056602933, 0.143938486292, 0.942999335737)-25.643877311, 52.8344935464, -121.035712713
12given(-0.917196282304, 0.39837425766, -0.00699503830006), (-0.398326441779, -0.916392475071, 0.0395079411284), (0.0093287462577, 0.0390228454407, 0.999194771817)-23.9005650093, 119.785663351, -129.820922245
13given(0.188075365833, -0.950670219383, -0.246685611145), (0.953278475237, 0.237150481802, -0.18713577325), (0.236406018147, -0.199964454241, 0.950855620809)34.3727461125, 76.26447981, -132.040154424
14given(0.523716739955, 0.786704903323, -0.326827433637), (-0.796969215989, 0.587985042903, 0.138252154012), (0.300933290045, 0.188066436158, 0.934917199827)-28.0148047544, 61.0147524104, -158.682678726
15given(-0.999615350749, -0.0247285362661, 0.0125558767188), (0.0247691632734, -0.999688420004, 0.00309054360127), (0.0124755399393, 0.00340035338648, 0.999916395755)-0.347564491722, 121.731934828, -165.28833772
16given(-0.112406761706, 0.967785858675, 0.22528926222), (-0.96265142076, -0.16226316629, 0.216732339476), (0.246306642281, -0.19251284792, 0.949879908911)-64.0844515571, 41.6161833293, -140.46078306
17given(0.889850463308, -0.456120230993, 0.0109766948632), (0.456195579414, 0.889103009659, -0.037167614092), (0.00719348828612, 0.038081138293, 0.999248758134)-3.79260717895, 2.62084695654, -137.712757023
18given(-0.847162819664, -0.400150076268, 0.349564119215), (0.412474480821, -0.90999767912, -0.0420597987128), (0.334932768852, 0.108554780915, 0.93596789469)-6.61763278918, 73.0054737527, -127.738226242
19given(0.316355903124, 0.942156971423, 0.110721198323), (-0.934050139295, 0.288969728033, 0.20987337507), (0.165738588872, -0.169813831828, 0.971439129683)-52.780124336, 25.9358136123, -105.058747179
20given(0.618124298584, -0.785491735335, 0.0304152136478), (0.782622414858, 0.611319103994, -0.117435551916), (0.0736512543094, 0.0963933961103, 0.992614631126)17.3054273986, 17.1077811423, -102.92121012
21given(-0.949731907531, 0.0468930812664, 0.30953245831), (-0.0410186334894, -0.998833868165, 0.0254632188377), (0.310365551447, 0.0114866329381, 0.950547885032)-14.2127329572, 78.186554236, -87.4000259914
22given(0.672983479441, 0.739458553101, -0.0171547266004), (-0.734659849131, 0.670948055688, 0.10051672818), (0.0858378848405, -0.0550432086162, 0.994787466101)-35.065888929, 17.1659936249, -72.5955343285
23given(0.221135431729, -0.971970610886, 0.079826389168), (0.952920208619, 0.197935912705, -0.229705138095), (0.2074661342, 0.126864124302, 0.969981080808)30.604881845, 38.4832636803, -67.306572617
24given(-0.826557402149, 0.452843086717, 0.334269352119), (-0.459651076789, -0.885829202129, 0.0634626840166), (0.324844191205, -0.101191716405, 0.940338496485)-27.9275748023, 75.3142093526, -45.4669870503
25given(0.899355586826, 0.43659569178, -0.0233180265913), (-0.4366403459, 0.899629690897, 0.00340992510468), (0.0224663476646, 0.00711485600295, 0.99972228246)-20.2525063696, 10.4050334091, -37.6059626649
26given(-0.188710124777, -0.962570888604, 0.194539901355), (0.946017579489, -0.23134346491, -0.227004274279), (0.263513240853, 0.14120016167, 0.954265836253)32.6789368085, 52.6715608907, -30.0101736117
27given(-0.566940042526, 0.764116341397, 0.307742107926), (-0.772017836499, -0.623173931387, 0.125070825406), (0.287345520775, -0.166674737286, 0.94321369988)-34.6280225, 62.6750063662, -5.5423977851

-
Components

#1: Protein ...
Nucleoprotein / Nucleocapsid protein


Mass: 14277.541 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengla dianlovirus / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q1NMU1

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M NaCl, 0.1M Cacodylate, 2M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.73→173.13 Å / Num. obs: 8223 / % possible obs: 84.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 108.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.131 / Net I/σ(I): 4.7
Reflection shellResolution: 3.73→4.27 Å / Rmerge(I) obs: 0.787 / Num. unique obs: 1356 / CC1/2: 0.785

-
Processing

Software
NameVersionClassification
REFMACdev_4788refinement
PHENIXdev_4788refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.73→173.13 Å / SU ML: 0.6382 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.7101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2651 435 5.29 %
Rwork0.2476 7788 -
obs0.2486 8223 25.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.41 Å2
Refinement stepCycle: LAST / Resolution: 3.73→173.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15048 0 0 0 15048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003215453
X-RAY DIFFRACTIONf_angle_d0.668321030
X-RAY DIFFRACTIONf_chiral_restr0.04192252
X-RAY DIFFRACTIONf_plane_restr0.01712792
X-RAY DIFFRACTIONf_dihedral_angle_d12.88635919
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2LX-RAY DIFFRACTIONTorsion NCS0.784923582045
ens_1d_3LX-RAY DIFFRACTIONTorsion NCS0.798719456123
ens_1d_4LX-RAY DIFFRACTIONTorsion NCS0.675923407061
ens_1d_5LX-RAY DIFFRACTIONTorsion NCS0.826630921211
ens_1d_6LX-RAY DIFFRACTIONTorsion NCS0.805857150338
ens_1d_7LX-RAY DIFFRACTIONTorsion NCS0.811078740701
ens_1d_8LX-RAY DIFFRACTIONTorsion NCS0.784054443384
ens_1d_9LX-RAY DIFFRACTIONTorsion NCS0.926715230479
ens_1d_10LX-RAY DIFFRACTIONTorsion NCS0.739483302618
ens_1d_11LX-RAY DIFFRACTIONTorsion NCS0.79792303627
ens_1d_12LX-RAY DIFFRACTIONTorsion NCS0.752296108069
ens_1d_13LX-RAY DIFFRACTIONTorsion NCS0.721092738301
ens_1d_14LX-RAY DIFFRACTIONTorsion NCS0.787725750973
ens_1d_15LX-RAY DIFFRACTIONTorsion NCS0.669272953873
ens_1d_16LX-RAY DIFFRACTIONTorsion NCS0.697262522531
ens_1d_17LX-RAY DIFFRACTIONTorsion NCS0.80462430892
ens_1d_18LX-RAY DIFFRACTIONTorsion NCS0.762027677722
ens_1d_19LX-RAY DIFFRACTIONTorsion NCS0.791512826946
ens_1d_20LX-RAY DIFFRACTIONTorsion NCS0.729053669311
ens_1d_21LX-RAY DIFFRACTIONTorsion NCS0.716949588387
ens_1d_22LX-RAY DIFFRACTIONTorsion NCS0.766151753258
ens_1d_23LX-RAY DIFFRACTIONTorsion NCS0.724298579366
ens_1d_24LX-RAY DIFFRACTIONTorsion NCS0.757800222554
ens_1d_25LX-RAY DIFFRACTIONTorsion NCS0.786122598908
ens_1d_26LX-RAY DIFFRACTIONTorsion NCS0.781601449444
ens_1d_27LX-RAY DIFFRACTIONTorsion NCS0.788957031266
ens_1d_28LX-RAY DIFFRACTIONTorsion NCS0.74210637722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.73-4.270.2862200.369381X-RAY DIFFRACTION3.69
4.27-5.380.3692950.30661415X-RAY DIFFRACTION13.89
5.38-173.130.24793200.23565992X-RAY DIFFRACTION57.21
Refinement TLS params.
IDMethodRefine-ID
1refinedX-RAY DIFFRACTION
2refinedX-RAY DIFFRACTION
3refinedX-RAY DIFFRACTION
4refinedX-RAY DIFFRACTION
5refinedX-RAY DIFFRACTION
6refinedX-RAY DIFFRACTION
7refinedX-RAY DIFFRACTION
8refinedX-RAY DIFFRACTION
9refinedX-RAY DIFFRACTION
10refinedX-RAY DIFFRACTION
11refinedX-RAY DIFFRACTION
12refinedX-RAY DIFFRACTION
13refinedX-RAY DIFFRACTION
14refinedX-RAY DIFFRACTION
15refinedX-RAY DIFFRACTION
16refinedX-RAY DIFFRACTION
17refinedX-RAY DIFFRACTION
18refinedX-RAY DIFFRACTION
19refinedX-RAY DIFFRACTION
20refinedX-RAY DIFFRACTION
21refinedX-RAY DIFFRACTION
22refinedX-RAY DIFFRACTION
23refinedX-RAY DIFFRACTION
24refinedX-RAY DIFFRACTION
25refinedX-RAY DIFFRACTION
26refinedX-RAY DIFFRACTION
27refinedX-RAY DIFFRACTION
28refinedX-RAY DIFFRACTION
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 633 through 697 )
2X-RAY DIFFRACTION2chain 'L' and (resid 634 through 697 )
3X-RAY DIFFRACTION3chain 'K' and (resid 634 through 697 )
4X-RAY DIFFRACTION4chain 'V' and (resid 632 through 697 )
5X-RAY DIFFRACTION5chain 'H' and (resid 635 through 697 )
6X-RAY DIFFRACTION6chain 'Z' and (resid 633 through 697 )
7X-RAY DIFFRACTION7chain 'B' and (resid 634 through 697 )
8X-RAY DIFFRACTION8chain 'Y' and (resid 633 through 697 )
9X-RAY DIFFRACTION9chain 'G' and (resid 632 through 697 )
10X-RAY DIFFRACTION10chain 'C' and (resid 634 through 697 )
11X-RAY DIFFRACTION11chain 'T' and (resid 634 through 697 )
12X-RAY DIFFRACTION12chain 'P' and (resid 636 through 697 )
13X-RAY DIFFRACTION13chain 'M' and (resid 631 through 697 )
14X-RAY DIFFRACTION14chain 'N' and (resid 632 through 697 )
15X-RAY DIFFRACTION15chain 'S' and (resid 636 through 697 )
16X-RAY DIFFRACTION16chain 'I' and (resid 633 through 697 )
17X-RAY DIFFRACTION17chain 'A' and (resid 632 through 697 )
18X-RAY DIFFRACTION18chain 'X' and (resid 632 through 697 )
19X-RAY DIFFRACTION19chain 'W' and (resid 632 through 697 )
20X-RAY DIFFRACTION20chain 'J' and (resid 632 through 697 )
21X-RAY DIFFRACTION21chain 'F' and (resid 634 through 697 )
22X-RAY DIFFRACTION22chain 'Q' and (resid 6333 through 697 )
23X-RAY DIFFRACTION23chain 'R' and (resid 635 through 697 )
24X-RAY DIFFRACTION24chain 'U' and (resid 634 through 697 )
25X-RAY DIFFRACTION25chain 'a' and (resid 634 through 697 )
26X-RAY DIFFRACTION26chain 'b' and (resid 634 through 697 )
27X-RAY DIFFRACTION27chain 'O' and (resid 633 through 697 )
28X-RAY DIFFRACTION28chain 'D' and (resid 634 through 697 )

+
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