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- PDB-6s53: Crystal structure of TRIM21 RING domain in complex with an isopep... -

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Basic information

Entry
Database: PDB / ID: 6s53
TitleCrystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate
Components
  • E3 ubiquitin-protein ligase TRIM21
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 N
KeywordsLIGASE / E3 ubiquitin ligase / E2 conjugating enzyme / intracellular immunity / viral defence / TRIM21 / Ube2N / ubiquitin
Function / homology
Function and homology information


negative regulation of protein deubiquitination / : / 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 ...negative regulation of protein deubiquitination / : / 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 / postreplication repair / stress granule disassembly / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / E2 ubiquitin-conjugating enzyme / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / response to type II interferon / protein monoubiquitination / 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 / 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 / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA
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. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / E3 ubiquitin-protein ligase TRIM21 / Ubiquitin-conjugating enzyme E2 N
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKiss, L. / Boland, A. / Neuhaus, D. / James, L.C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105181010 United Kingdom
Medical Research Council (United Kingdom)U105178934 United Kingdom
Wellcome TrustInvestigator Award to Leo C James United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: A tri-ionic anchor mechanism drives Ube2N-specific recruitment and K63-chain ubiquitination in TRIM ligases.
Authors: Kiss, L. / Zeng, J. / Dickson, C.F. / Mallery, D.L. / Yang, J.C. / McLaughlin, S.H. / Boland, A. / Neuhaus, D. / James, L.C.
History
DepositionJun 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_asym_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
E: Ubiquitin-conjugating enzyme E2 N
F: Polyubiquitin-C
C: Ubiquitin-conjugating enzyme E2 N
D: Polyubiquitin-C
B: E3 ubiquitin-protein ligase TRIM21
A: E3 ubiquitin-protein ligase TRIM21
K: Ubiquitin-conjugating enzyme E2 N
L: Polyubiquitin-C
I: Ubiquitin-conjugating enzyme E2 N
J: Polyubiquitin-C
H: E3 ubiquitin-protein ligase TRIM21
G: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,49221
Polymers140,85012
Non-polymers6419
Water1086
1
E: Ubiquitin-conjugating enzyme E2 N
F: Polyubiquitin-C
C: Ubiquitin-conjugating enzyme E2 N
D: Polyubiquitin-C
B: E3 ubiquitin-protein ligase TRIM21
A: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,80511
Polymers70,4256
Non-polymers3805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: Ubiquitin-conjugating enzyme E2 N
L: Polyubiquitin-C
I: Ubiquitin-conjugating enzyme E2 N
J: Polyubiquitin-C
H: E3 ubiquitin-protein ligase TRIM21
G: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,68710
Polymers70,4256
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.750, 83.310, 86.750
Angle α, β, γ (deg.)89.90, 89.05, 88.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21C
12E
22K
13E
23I
14F
24D
15F
25L
16F
26J
17C
27K
18C
28I
19D
29L
110D
210J
111B
211A
112B
212H
113B
213G
114A
214H
115A
215G
116K
216I
117L
217J
118H
218G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROASNASNEA5 - 1515 - 151
21PROPROASNASNCC5 - 1515 - 151
12PROPROASNASNEA5 - 1515 - 151
22PROPROASNASNKG5 - 1515 - 151
13PROPROASNASNEA5 - 1515 - 151
23PROPROASNASNII5 - 1515 - 151
14METMETGLYGLYFB1 - 761 - 76
24METMETGLYGLYDD1 - 761 - 76
15METMETGLYGLYFB1 - 761 - 76
25METMETGLYGLYLH1 - 761 - 76
16METMETGLYGLYFB1 - 761 - 76
26METMETGLYGLYJJ1 - 761 - 76
17LEULEUILEILECC4 - 1524 - 152
27LEULEUILEILEKG4 - 1524 - 152
18LEULEUILEILECC4 - 1524 - 152
28LEULEUILEILEII4 - 1524 - 152
19METMETGLYGLYDD1 - 761 - 76
29METMETGLYGLYLH1 - 761 - 76
110METMETGLYGLYDD1 - 761 - 76
210METMETGLYGLYJJ1 - 761 - 76
111SERSERGLNGLNBE3 - 813 - 81
211SERSERGLNGLNAF3 - 813 - 81
112ARGARGSERSERBE6 - 806 - 80
212ARGARGSERSERHK6 - 806 - 80
113SERSERSERSERBE3 - 803 - 80
213SERSERSERSERGL3 - 803 - 80
114ARGARGSERSERAF6 - 806 - 80
214ARGARGSERSERHK6 - 806 - 80
115SERSERSERSERAF3 - 803 - 80
215SERSERSERSERGL3 - 803 - 80
116LEULEUILEILEKG4 - 1524 - 152
216LEULEUILEILEII4 - 1524 - 152
117METMETGLYGLYLH1 - 761 - 76
217METMETGLYGLYJJ1 - 761 - 76
118ARGARGSERSERHK6 - 806 - 80
218ARGARGSERSERGL6 - 806 - 80

NCS ensembles :
IDDetails
1E, C
2E, K
3E, I
4F, D
5F, L
6F, J
7C, K
8C, I
9D, L
10D, J
11B, A
12B, H
13B, G
14A, H
15A, G
16K, I
17L, J
18H, G

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Components

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Protein , 3 types, 12 molecules ECKIFDLJBAHG

#1: 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: 17125.705 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#2: Protein
Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 / References: UniProt: P0CG48
#3: Protein
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: 9510.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM21, RNF81, RO52, SSA1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P19474, RING-type E3 ubiquitin transferase

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Non-polymers , 3 types, 15 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→19.76 Å / Num. obs: 32828 / % possible obs: 95.74 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03857 / Rpim(I) all: 0.03857 / Rrim(I) all: 0.05454 / Net I/σ(I): 12.83
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.3994 / Num. unique obs: 3279 / CC1/2: 0.735 / Rpim(I) all: 0.3994 / Rrim(I) all: 0.5649

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OLM, 5EYA

5olm

5eya


Resolution: 2.8→19.76 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.046 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 2003 6.1 %RANDOM
Rwork0.2092 ---
obs-32828 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å21.96 Å2-0.31 Å2
2---0.84 Å22.67 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.8→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9443 0 16 6 9465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0149650
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178876
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.66113100
X-RAY DIFFRACTIONr_angle_other_deg0.8271.6320865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53851205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.25122.495485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.489151695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6051568
X-RAY DIFFRACTIONr_chiral_restr0.0540.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210733
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021595
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2287.6264847
X-RAY DIFFRACTIONr_mcbond_other5.2267.6254846
X-RAY DIFFRACTIONr_mcangle_it7.98511.436037
X-RAY DIFFRACTIONr_mcangle_other7.98511.4316038
X-RAY DIFFRACTIONr_scbond_it5.5698.0574803
X-RAY DIFFRACTIONr_scbond_other5.5688.0584804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5611.8957062
X-RAY DIFFRACTIONr_long_range_B_refined11.41390.74710445
X-RAY DIFFRACTIONr_long_range_B_other11.41290.75210446
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11E44470.1
12C44470.1
21E44110.1
22K44110.1
31E43950.11
32I43950.11
41F21060.15
42D21060.15
51F21310.11
52L21310.11
61F20740.13
62J20740.13
71C44630.1
72K44630.1
81C44880.11
82I44880.11
91D20990.13
92L20990.13
101D20650.11
102J20650.11
111B22760.12
112A22760.12
121B21270.09
122H21270.09
131B21710.11
132G21710.11
141A21460.09
142H21460.09
151A22260.09
152G22260.09
161K44230.1
162I44230.1
171L20520.1
172J20520.1
181H20730.09
182G20730.09
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.3655 197 -
Rwork0.3203 3279 -
obs--96.05 %

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