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- PDB-7bbd: Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In c... -

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Basic information

Entry
Database: PDB / ID: 7bbd
TitleCrystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2
Components
  • (Polyubiquitin- ...) x 2
  • (Ubiquitin-conjugating enzyme E2 ...) x 2
KeywordsLIGASE / E3 ubiquitin ligase / E2 conjugating enzyme / ubiquitin chain elongation
Function / homology
Function and homology information


negative regulation of protein deubiquitination / error-free postreplication DNA repair / : / UBC13-MMS2 complex / regulation of viral entry into host cell / protein K27-linked ubiquitination / ubiquitin conjugating enzyme complex / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination ...negative regulation of protein deubiquitination / error-free postreplication DNA repair / : / UBC13-MMS2 complex / regulation of viral entry into host cell / protein K27-linked ubiquitination / ubiquitin conjugating enzyme complex / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / regulation of type I interferon production / cellular response to chemical stress / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses / hypothalamus gonadotrophin-releasing hormone neuron development / postreplication repair / stress granule disassembly / female meiosis I / positive regulation of double-strand break repair / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / positive regulation of intracellular signal transduction / fat pad development / E2 ubiquitin-conjugating enzyme / female gonad development / negative regulation of NF-kappaB transcription factor activity / seminiferous tubule development / male meiosis I / pyroptotic inflammatory response / response to type II interferon / protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response / autophagosome / proteasomal protein catabolic process / protein autoubiquitination / protein K48-linked ubiquitination / regulation of DNA repair / positive regulation of autophagy / positive regulation of cell cycle / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / negative regulation of TORC1 signaling / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / positive regulation of DNA repair / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / negative regulation of innate immune response / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / neuron projection morphogenesis
Similarity search - Function
TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / zinc finger of C3HC4-type, RING / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Modified RING finger domain / U-box domain / B-box zinc finger ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / zinc finger of C3HC4-type, RING / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Modified RING finger domain / U-box domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin B / Polyubiquitin-B / Polyubiquitin-C / E3 ubiquitin-protein ligase TRIM21 / Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKiss, L. / Neuhaus, D. / James, L.C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105181010 United Kingdom
Medical Research Council (MRC, United Kingdom)U105178934 United Kingdom
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination.
Authors: Kiss, L. / Clift, D. / Renner, N. / Neuhaus, D. / James, L.C.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Polyubiquitin-B,E3 ubiquitin-protein ligase TRIM21
D: Polyubiquitin-C
A: Ubiquitin-conjugating enzyme E2 variant 2
C: Ubiquitin-conjugating enzyme E2 N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1996
Polymers61,0684
Non-polymers1312
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.150, 108.360, 75.140
Angle α, β, γ (deg.)90.000, 104.990, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11B-328-

HOH

21B-366-

HOH

31A-209-

HOH

41C-248-

HOH

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Components

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Polyubiquitin- ... , 2 types, 2 molecules BD

#1: Protein Polyubiquitin-B,E3 ubiquitin-protein ligase TRIM21 / 52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / RING- ...52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / RING-type E3 ubiquitin transferase TRIM21 / Ro(SS-A) / Sjoegren syndrome type A antigen / SS-A / Tripartite motif-containing protein 21


Mass: 18379.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB, TRIM21, RNF81, RO52, SSA1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: J3QS39, UniProt: P19474, UniProt: P0CG47*PLUS, RING-type E3 ubiquitin transferase
#2: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 1 / Mutation: G75A, G76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48

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Ubiquitin-conjugating enzyme E2 ... , 2 types, 2 molecules AC

#3: Protein Ubiquitin-conjugating enzyme E2 variant 2 / DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation- ...DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation-promoting factor 1 / EDPF-1 / MMS2 homolog / Vitamin D3-inducible protein


Mass: 16929.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V2, MMS2, UEV2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15819
#4: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17182.756 Da / Num. of mol.: 1 / Mutation: C87K, K92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme

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Non-polymers , 2 types, 287 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop
Details: MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2019 / Details: Eiger2 XE 16M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→19.99 Å / Num. obs: 38727 / % possible obs: 99.41 % / Redundancy: 7.1 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04551 / Rpim(I) all: 0.01839 / Rrim(I) all: 0.04914 / Net I/σ(I): 20.18
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.9457 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 3856 / CC1/2: 0.932 / % possible all: 99.15

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S53, 1UBQ, 1J74
Resolution: 2.2→19.99 Å / SU ML: 0.2935 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.6248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 2004 5.18 %
Rwork0.222 36716 -
obs0.2236 38720 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4147 0 2 285 4434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214225
X-RAY DIFFRACTIONf_angle_d0.52555727
X-RAY DIFFRACTIONf_chiral_restr0.0431651
X-RAY DIFFRACTIONf_plane_restr0.0038748
X-RAY DIFFRACTIONf_dihedral_angle_d17.5311604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.33631500.32912583X-RAY DIFFRACTION99.02
2.25-2.320.32681230.30922658X-RAY DIFFRACTION99.29
2.32-2.380.33461530.29912571X-RAY DIFFRACTION99.2
2.38-2.460.30331350.27912609X-RAY DIFFRACTION99.28
2.46-2.550.28991550.26042586X-RAY DIFFRACTION99.35
2.55-2.650.30881300.26342626X-RAY DIFFRACTION99.49
2.65-2.770.28331520.24772613X-RAY DIFFRACTION99.57
2.77-2.920.26221370.23592619X-RAY DIFFRACTION99.53
2.92-3.10.30541380.22292630X-RAY DIFFRACTION99.78
3.1-3.340.26211510.21652622X-RAY DIFFRACTION99.82
3.34-3.670.2271370.20312663X-RAY DIFFRACTION99.93
3.67-4.20.2111440.1742610X-RAY DIFFRACTION99.96
4.2-5.270.19221480.17082658X-RAY DIFFRACTION99.96
5.27-19.990.20371510.18272668X-RAY DIFFRACTION99.72
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.583196084921.002829697213.01366579980.212563355225-0.01159667000375.12239418703-0.2263508381160.3958031490880.576382918632-0.2281357894630.01217561961230.274273924681-0.1465243944810.03842495263450.1715571032990.109571740408-0.00496969778859-0.03187830601260.1074217498180.02418291417080.139151036171-25.932152888747.5868151316-14.3319015028
28.804564323682.932041745111.566495063683.71424159139-0.2497577564170.6425873587670.0004669231729720.484091011248-0.294397741608-0.4961595318010.07845775809240.01887251234550.3738368672740.276828969329-0.09110169661510.1922889349520.03908244178840.002263534980520.123499116375-0.0001443343340670.0536245117797-19.563381718639.2254027275-13.881922155
31.46420443808-0.174965727288-0.07177054114470.06373425035410.180472306520.696885924694-0.1756625892290.334865155760.721409272973-0.0492089240326-0.0446723965669-0.184442560972-0.3338853333150.192228389749-0.1060342267640.174645407458-0.0890271140967-0.04718288977650.09336773942110.1798353657240.404608040048-6.6112056195152.6157480553-7.01540273358
43.096141182970.655093618744-1.246935596186.02922988406-1.937516083224.060726310050.1820335012310.0993666536609-0.277076723460.0118772733414-0.151960067921-0.2391593378650.2822281795280.06454286622020.08393811614950.1249905884450.0258212861264-0.04795443508260.04214069285990.01890574717780.155161555064-3.2366821576437.8680624808-3.30252289389
53.23895751608-0.2039938569530.6644865132272.43496309688-0.2119938697013.51620063527-0.173369136370.0816548936966-0.0435812231208-0.118222597373-0.07077902012640.3815779021970.0789569759579-0.3577851252470.2000785748020.180934394376-0.0579909849823-0.07683878543880.31316535495-0.00619667142940.185264625457-40.001448955641.51239348-27.9435139446
60.587003551493-0.6959684400130.2969545040861.44437899537-0.8465836194590.6451687677840.1924446651791.25277433547-0.11383348397-0.773662893148-0.321364360866-0.398669439050.3930675030731.29602170119-0.1431970234610.4661166556030.2305111487360.02032634637781.10353273286-0.1083132772730.285337720916-16.567850161138.0299018752-28.881758346
74.019467184870.462786545372-0.1898857580852.09091377060.1062919544961.68573218851-0.0344672740674-0.8348700649680.7954159073570.3133440905090.07715201489930.370506023411-0.0671946436014-0.2053811476850.03523326955450.1769279243260.08970397212870.1344578951320.722846770252-0.2608349755680.265230042965-34.103072748247.30195508685.88071623614
81.69506611493-0.81719231086-0.340291816231.50960295942-0.9754108940972.34466365281.60902106851E-5-1.211476231350.7165609997850.8098666652380.165952457103-0.0346175198347-0.3928320472560.191138112791-0.2603174626440.530810943092-0.09804251078480.07747891355751.37946225573-0.3438255033760.335795248966-24.624674148750.601024198918.6326027925
90.653401132285-0.361770303522-0.2373620480481.619741563860.4576832355960.160423471272-0.252069678038-0.4238540273370.05068201779281.143578028440.2848411616920.163726939278-0.133183459421-0.252601083799-0.04235999215511.30073795953-0.2068735268990.2392870872972.01819037049-0.4617978559880.65765715493-26.047371806350.532789129530.6040838824
101.11036410613-0.367746466175-0.6823537939141.22151163197-1.406567686633.664488284220.00285851961371-0.4562925468340.3308498300390.7446955292090.3296673527720.127519028766-0.651896926701-0.00772382411153-0.4080328983020.818565843141-0.09138265275620.3872380855861.90312784428-0.6244452951560.734061963067-32.493332298454.448178192425.3106612425
114.70933342922-1.377335786781.806871339463.18281085815-0.8827904555861.887493450110.2840801639670.267894864185-1.1060706781-0.1039561928490.09014434800970.1741512498650.493112012948-0.146046108572-0.05453184875650.268624425723-0.0155919059547-0.08092690950510.21582284836-0.1211545221090.472384712119-32.115757535130.7005626406-11.7166405195
123.67126703773-1.405214742110.1421075648421.123287839910.7513522035561.110667810980.0797794543706-0.39621655739-0.5340371207710.2973334388130.02621343715970.3643363179860.389690492366-0.3310888932280.3893143356350.162495972234-0.1336186073280.02888542395550.09880331308670.1458789515190.336979699301-27.828093550632.6956545293-2.82626181301
132.353494714460.0915209756395-0.5189299858581.78614978535-0.7218809065211.954875860540.1608277169140.105891441466-0.2663496556970.04065519417350.03605088142390.1404203200690.283530493162-0.171506052970.2494802900240.1554214737190.0158435466655-0.0129178466606-0.00513325248962-0.1009041900090.0830718079494-21.086137834638.9811388115-8.49991562004
143.361646825470.2575027800080.330615050741.69926526356-0.9024723319011.153951907060.0790388143493-0.2543816843430.05923261884360.3856277498180.005510452924150.128433006508-0.0270877270715-0.14510055881-0.05258683530870.197427300357-0.05050251007230.05578302983050.00140382260730.01877299306410.0659071722336-15.327640823144.2028617291-1.79106837462
150.517562533232-0.107175660778-0.8942568479311.92866724320.4220859939713.814844281490.1668195523780.2624059662750.818181082634-0.2552857270910.0440280735214-0.391863642071-0.971357243950.2853367656490.6647696309270.450092197265-0.148152395419-0.1527031362570.3702354902610.6545953107191.01423152525-36.477808720611.8883324749-11.4446295997
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 87 through 100 )CF87 - 10088 - 101
22chain 'C' and (resid 101 through 112 )CF101 - 112102 - 113
33chain 'C' and (resid 113 through 132 )CF113 - 132114 - 133
44chain 'C' and (resid 133 through 152 )CF133 - 152134 - 153
55chain 'B' and (resid 82 through 158 )BA82 - 15884 - 160
66chain 'D' and (resid 1 through 76 )DD1 - 761 - 76
77chain 'A' and (resid -4 through 35 )AE-4 - 351 - 40
88chain 'A' and (resid 36 through 78 )AE36 - 7841 - 83
99chain 'A' and (resid 79 through 98 )AE79 - 9884 - 103
1010chain 'A' and (resid 99 through 144 )AE99 - 144104 - 149
1111chain 'C' and (resid 0 through 27 )CF0 - 271 - 28
1212chain 'C' and (resid 28 through 40 )CF28 - 4029 - 41
1313chain 'C' and (resid 41 through 67 )CF41 - 6742 - 68
1414chain 'C' and (resid 68 through 86 )CF68 - 8669 - 87
1515chain 'B' and (resid -1 through 81 )BA-1 - 811 - 83

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