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- PDB-9tnz: SP100 CARD filament -

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Basic information

Entry
Database: PDB / ID: 9tnz
TitleSP100 CARD filament
ComponentsMaltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
KeywordsIMMUNE SYSTEM / Innate immunity / interferon / DNA damage / cryo-EM
Function / homology
Function and homology information


regulation of Fas signaling pathway / regulation of viral process / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway ...regulation of Fas signaling pathway / regulation of viral process / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / regulation of angiogenesis / maltose transport / maltodextrin transmembrane transport / type II interferon-mediated signaling pathway / response to retinoic acid / response to type II interferon / SUMOylation of DNA damage response and repair proteins / retinoic acid receptor signaling pathway / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to cytokine / nuclear periphery / ATP-binding cassette (ABC) transporter complex / telomere maintenance / cell chemotaxis / DNA damage response, signal transduction by p53 class mediator / PML body / kinase binding / Interferon gamma signaling / transcription corepressor activity / outer membrane-bounded periplasmic space / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / periplasmic space / chromosome, telomeric region / protein dimerization activity / nuclear body / protein domain specific binding / negative regulation of DNA-templated transcription / DNA damage response / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm
Similarity search - Function
HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain ...HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Nuclear autoantigen Sp-100
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsRabl, J. / Aird, E. / Corn, J.
Funding supportEuropean Union, Switzerland, 3items
OrganizationGrant numberCountry
European Research Council (ERC)855741-DDREAMM-ERC-2019-SyGEuropean Union
Swiss National Science Foundation310030_188858 Switzerland
European Molecular Biology Organization (EMBO)ALTF 144-2021European Union
Citation
Journal: To Be Published
Title: SP100 CARD filament
Authors: Rabl, J. / Aird, E. / Corn, J.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionDec 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
B: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
C: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
D: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
E: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
F: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
G: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
H: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
I: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
J: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
K: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
L: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
M: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
N: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
O: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
P: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
Q: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
R: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
S: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
T: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
V: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
W: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
X: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
Y: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
Z: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
AA: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100


Theoretical massNumber of molelcules
Total (without water)1,530,72826
Polymers1,530,72826
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "E"
d_2ens_1chain "AA"
d_3ens_1chain "B"
d_4ens_1chain "C"
d_5ens_1chain "D"
d_6ens_1chain "R"
d_7ens_1chain "F"
d_8ens_1chain "G"
d_9ens_1chain "H"
d_10ens_1chain "I"
d_11ens_1chain "J"
d_12ens_1chain "K"
d_13ens_1chain "L"
d_14ens_1chain "M"
d_15ens_1chain "N"
d_16ens_1chain "O"
d_17ens_1chain "P"
d_18ens_1chain "Q"
d_19ens_1chain "A"
d_20ens_1chain "S"
d_21ens_1chain "T"
d_22ens_1chain "V"
d_23ens_1chain "W"
d_24ens_1chain "X"
d_25ens_1chain "Y"
d_26ens_1chain "Z"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 49 - 147 / Label seq-ID: 425 - 523

Dom-IDAuth asym-IDLabel asym-ID
d_1EE
d_2AAZ
d_3BB
d_4CC
d_5DD
d_6RR
d_7FF
d_8GG
d_9HH
d_10II
d_11JJ
d_12KK
d_13LL
d_14MM
d_15NN
d_16OO
d_17PP
d_18QQ
d_19AA
d_20SS
d_21TT
d_22VU
d_23WV
d_24XW
d_25YX
d_26ZY

NCS oper:
IDCodeMatrixVector
1given(-0.172615883464, -0.984987399263, -0.00189210729097), (-0.984983616287, 0.172608105894, 0.00370370436702), (-0.00332150907647, 0.00250301288326, -0.999991351215)326.514141748, 273.36419347, 209.123391131
2given(-0.758592913092, 0.651563886137, 0.00113775628435), (-0.651561486722, -0.758593441608, 0.00190246423749), (0.00210267144727, 0.000701877711815, 0.999997543067)167.211636453, 364.090217388, -60.1545905381
3given(-0.0505249348174, 0.998722778621, 0.00020597320236), (-0.998721357783, -0.0505252112601, 0.0016889448361), (0.00169719451921, -0.000120376008574, 0.999998552519)7.80750662643, 309.574613699, -40.0567311042
4given(0.688959758259, 0.724799559089, -0.00022504348797), (-0.724799142598, 0.68895964248, 0.000902177139646), (0.000808943474049, -0.00045845241691, 0.999999567716)-62.5238814399, 156.470834925, -19.9784766318
5given(-0.995559863717, 0.0941234855957, 0.00115204791032), (-0.0941239074518, -0.995560439776, -0.000317488880137), (0.00111705016421, -0.000424514437132, 0.999999285993)287.302939785, 316.003687236, 79.4178759826
6given(-0.708512663542, -0.705686256354, 0.00408817715495), (-0.705694947586, 0.708514921885, -0.00111643068944), (-0.00210868472389, -0.00367601124452, -0.999991020155)364.261661833, 151.137604912, 349.11865998
7given(-0.999620674693, 0.0272820623908, 0.00376773109275), (0.0272745954468, 0.999625939704, -0.00201918654983), (-0.00382140930758, -0.00191565727997, -0.999990863502)297.574882931, -3.62579787694, 329.194000295
8given(-0.669010207803, 0.743247514196, 0.00291109892972), (0.743243751242, 0.669016322974, -0.00242607368531), (-0.00375074593764, 0.000540588028412, -0.999992819809)139.51557749, -61.8732120955, 308.908629922
9given(0.0777182228392, 0.996973342626, 0.00200796711739), (0.996973440338, -0.0777139579865, -0.00212131888226), (-0.00195885130463, 0.00216675501872, -0.999995734028)-11.5839161923, 12.5838919465, 288.465230839
10given(0.776066343336, 0.630649047288, 0.0016762742095), (0.630651035533, -0.776065623756, -0.00119122053554), (0.000549656694137, 0.00198161023118, -0.999997885547)-61.7152675178, 173.41372192, 268.21426733
11given(0.98091254353, 0.194429434821, -0.00278869527818), (-0.194430677832, 0.980916244853, -0.000179165834029), (0.00270064138846, 0.000717953927176, 0.999996095532)-26.0312588994, 32.3362024333, -159.671149262
12given(0.816784508159, -0.576939150357, -0.0020697864973), (0.576938958381, 0.816786922951, -0.000748865032944), (0.00212262410013, -0.000582479108209, 0.99999757759)115.290777337, -59.4117084136, -139.479723125
13given(0.144674022674, -0.989478755627, -0.00110423122302), (0.989479067511, 0.144674763261, -0.000622762049612), (0.000775964208677, -0.00100251618998, 0.99999919642)279.122688745, -20.1882959111, -119.299864502
14given(-0.617464554201, -0.786598530802, -0.00052501943347), (0.786598589203, -0.617464688718, 0.000132852802672), (-0.000428682780453, -0.000330947649095, 0.999999853352)363.583627417, 125.606897616, -99.3074674272
15given(0.693905109358, -0.72006642237, 0.000215829103718), (0.720064684424, 0.693902707572, -0.00242542151468), (0.00159670019337, 0.00183842329684, 0.99999703537)155.032293947, -62.1874799696, 19.2649383986
16given(-0.0438248838714, -0.999038572891, 0.00114430281654), (0.999036977772, -0.0438271875869, -0.00207235932277), (0.00212051847454, 0.00105237992083, 0.999997197945)308.636752073, 7.09067247689, 39.1994365051
17given(-0.754193770418, -0.656650161642, 0.00152377094471), (0.656649073694, -0.754195303597, -0.00119918669267), (0.00193666702584, 9.61636461831E-5, 0.999998120035)364.263304034, 166.128271348, 59.2954087061
18given(-0.994894830003, -0.10089799701, 0.00196759558284), (0.100900835018, -0.994895502028, 0.00140054885307), (0.00181623942118, 0.00159193085037, 0.999997083511)316.586090592, 286.07308762, -80.1678506253
19given(-0.117708753427, 0.993042984469, -0.00320630073218), (0.993045709841, 0.117700676095, -0.00260173287247), (-0.00220624881253, -0.00349024991972, -0.999991475275)19.5709411981, -16.3494155711, 448.550536445
20given(0.638645152963, 0.769492170023, -0.0037641559524), (0.769492008597, -0.638653874554, -0.00181031021089), (-0.00379701231602, -0.00174034208294, -0.999991276915)-60.9809956704, 131.678369858, 428.601822315
21given(0.997726144067, 0.0673067648019, -0.00351295571158), (0.0673041699367, -0.997732139932, -0.000851854500038), (-0.00356232439008, 0.000613480937436, -0.999993466722)-9.20748850156, 291.975378881, 408.307642608
22given(0.736260854901, -0.676692233334, -0.00275225097337), (-0.676695527633, -0.736262870223, -0.000385761054901), (-0.00176533869145, 0.00214645668867, -0.999996138144)142.669255561, 364.850063692, 387.871526682
23given(0.0168801786429, -0.999855892425, -0.00180387122131), (-0.999857337138, -0.0168790580563, -0.00063464182772), (0.000604102723954, 0.00181432674331, -0.999998171638)300.099257126, 304.957128946, 367.648942076
24given(0.992449766808, -0.122598702416, -0.00360811988718), (-0.12258500011, -0.992450736, 0.00380188905745), (-0.00404698790278, -0.00333088253173, -0.999986263461)20.2778015353, 318.965429998, 249.952450829
25given(0.594925539266, -0.803775943286, -0.00279923624707), (-0.803765455738, -0.594932092541, 0.00411064792283), (-0.00496939538968, -0.000195600034378, -0.999987633349)183.219772107, 361.891364296, 229.6856497

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Components

#1: Protein ...
Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Nuclear dot-associated Sp100 ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Nuclear dot-associated Sp100 protein / Speckled 100 kDa


Mass: 58874.168 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, SP100 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P23497
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: SP100 CARD domain filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES pH 8.01
2150 mMsodium chlorideNaCl1
30.05 %NP401
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7 sec. / Electron dose: 64 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10995
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.0particle selection
2EPUimage acquisition
4cryoSPARC4.4.0CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIX1.21rc1_4985model refinement
11cryoSPARC4.4.0initial Euler assignment
12cryoSPARC4.4.0final Euler assignment
13cryoSPARC4.4.0classification
14cryoSPARC4.4.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 46.4 ° / Axial rise/subunit: 19.8 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 2890408
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 296140 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingB value: 66.53 / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 66.53 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002421944
ELECTRON MICROSCOPYf_angle_d0.373129614
ELECTRON MICROSCOPYf_chiral_restr0.0363302
ELECTRON MICROSCOPYf_plane_restr0.0043822
ELECTRON MICROSCOPYf_dihedral_angle_d2.69162782
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EEELECTRON MICROSCOPYNCS constraints6.46126620131E-11
ens_1d_3EEELECTRON MICROSCOPYNCS constraints1.93873206652E-13
ens_1d_4EEELECTRON MICROSCOPYNCS constraints1.09589901709E-13
ens_1d_5EEELECTRON MICROSCOPYNCS constraints2.36732993394E-13
ens_1d_6EEELECTRON MICROSCOPYNCS constraints3.97240312129E-11
ens_1d_7EEELECTRON MICROSCOPYNCS constraints1.79010865028E-10
ens_1d_8EEELECTRON MICROSCOPYNCS constraints3.21563289005E-13
ens_1d_9EEELECTRON MICROSCOPYNCS constraints9.18313326927E-14
ens_1d_10EEELECTRON MICROSCOPYNCS constraints5.95084473263E-12
ens_1d_11EEELECTRON MICROSCOPYNCS constraints1.68953529956E-13
ens_1d_12EEELECTRON MICROSCOPYNCS constraints4.10712086942E-12
ens_1d_13EEELECTRON MICROSCOPYNCS constraints7.36405935112E-14
ens_1d_14EEELECTRON MICROSCOPYNCS constraints1.27187717962E-10
ens_1d_15EEELECTRON MICROSCOPYNCS constraints3.30539809483E-11
ens_1d_16EEELECTRON MICROSCOPYNCS constraints4.85837623069E-12
ens_1d_17EEELECTRON MICROSCOPYNCS constraints1.30478242475E-12
ens_1d_18EEELECTRON MICROSCOPYNCS constraints1.01926180885E-10
ens_1d_19EEELECTRON MICROSCOPYNCS constraints3.24861518437E-13
ens_1d_20EEELECTRON MICROSCOPYNCS constraints3.50824250742E-13
ens_1d_21EEELECTRON MICROSCOPYNCS constraints2.09022402778E-12
ens_1d_22EEELECTRON MICROSCOPYNCS constraints1.69027948165E-13
ens_1d_23EEELECTRON MICROSCOPYNCS constraints1.73319761127E-10
ens_1d_24EEELECTRON MICROSCOPYNCS constraints5.90251348938E-12
ens_1d_25EEELECTRON MICROSCOPYNCS constraints1.27442710509E-13
ens_1d_26EEELECTRON MICROSCOPYNCS constraints8.19241657522E-12

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