[English] 日本語
Yorodumi
- PDB-4lcd: Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin liga... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lcd
TitleStructure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3
Components
  • E3 ubiquitin-protein ligase RSP5
  • Protein SNA3
  • Ubiquitin
KeywordsLigase/protein binding / Ligase / E3 / Rsp5 / NEDD4 / Ubiquitin / HECT / Sna3 / thioester / maleimide / crosslink / Ligase-protein binding complex
Function / homology
Function and homology information


regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / fungal-type vacuole lumen / RHOQ GTPase cycle ...regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / fungal-type vacuole lumen / RHOQ GTPase cycle / positive regulation of ubiquitin-dependent endocytosis / RHOU GTPase cycle / cellular response to L-arginine / ubiquitin-dependent endocytosis / ribophagy / free ubiquitin chain polymerization / regulation of rRNA processing / mitochondria-associated ubiquitin-dependent protein catabolic process / regulation of mRNA export from nucleus / cellular bud tip / actin cortical patch / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / positive regulation of fatty acid biosynthetic process / regulation of nitrogen utilization / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / fungal-type vacuole / HECT-type E3 ubiquitin transferase / ubiquitin-ubiquitin ligase activity / poly(A)+ mRNA export from nucleus / Regulation of PTEN stability and activity / nonfunctional rRNA decay / cellular response to stress / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of endocytosis / Antigen processing: Ubiquitination & Proteasome degradation / protein K63-linked ubiquitination / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / cytosolic ribosome / 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 / 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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / phosphatidylinositol binding / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C
Similarity search - Function
Uncharacterized protein family UPF0057 signature. / Proteolipid membrane potential modulator / Proteolipid membrane potential modulator / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type ...Uncharacterized protein family UPF0057 signature. / Proteolipid membrane potential modulator / Proteolipid membrane potential modulator / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Protein SNA3 / E3 ubiquitin-protein ligase RSP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKamadurai, H.B. / Miller, D. / Schulman, B.A.
CitationJournal: Elife / Year: 2013
Title: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3.
Authors: Kamadurai, H.B. / Qiu, Y. / Deng, A. / Harrison, J.S. / Macdonald, C. / Actis, M. / Rodrigues, P. / Miller, D.J. / Souphron, J. / Lewis, S.M. / Kurinov, I. / Fujii, N. / Hammel, M. / Piper, ...Authors: Kamadurai, H.B. / Qiu, Y. / Deng, A. / Harrison, J.S. / Macdonald, C. / Actis, M. / Rodrigues, P. / Miller, D.J. / Souphron, J. / Lewis, S.M. / Kurinov, I. / Fujii, N. / Hammel, M. / Piper, R. / Kuhlman, B. / Schulman, B.A.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RSP5
B: E3 ubiquitin-protein ligase RSP5
C: Protein SNA3
D: Protein SNA3
E: Ubiquitin
F: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)125,2296
Polymers125,2296
Non-polymers00
Water00
1
A: E3 ubiquitin-protein ligase RSP5
C: Protein SNA3
E: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)62,6143
Polymers62,6143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RSP5
D: Protein SNA3
F: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)62,6143
Polymers62,6143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.046, 78.923, 96.722
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein E3 ubiquitin-protein ligase RSP5 / Reverses SPT-phenotype protein 5


Mass: 50470.703 Da / Num. of mol.: 2 / Fragment: WW3 + HECT (UNP residues 383-809) / Mutation: C455L, C517G, C721A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MDP1, NPI1, RSP5, SYGP-ORF41, YER125W / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli)
References: UniProt: P39940, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Protein SNA3


Mass: 2560.615 Da / Num. of mol.: 2 / Fragment: CYTOSOLIC FRAGMENT (UNP residues 104-127) / Mutation: K125A / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14359
#3: Protein Ubiquitin


Mass: 9582.997 Da / Num. of mol.: 2 / Fragment: UNP residues 1-75 / Mutation: G75C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC, UBIQUITIN / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / pH: 7.2
Details: 0.1M Bis Tris Propane, 21% w/v PEG3350, 1% w/v polypropylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2012
RadiationMonochromator: CRYO-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 21931 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.072 / Net I/σ(I): 15.5
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.361 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.4 Å / SU ML: 0.5 / σ(F): 1.35 / Phase error: 33.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.299 1088 5.1 %
Rwork0.251 --
obs0.253 21323 95 %
all-21931 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.4 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-26.4355 Å20 Å27.4434 Å2
2---25.3352 Å2-0 Å2
3----1.1004 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7944 0 0 0 7944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098125
X-RAY DIFFRACTIONf_angle_d1.04311020
X-RAY DIFFRACTIONf_dihedral_angle_d22.7684929
X-RAY DIFFRACTIONf_chiral_restr0.0641200
X-RAY DIFFRACTIONf_plane_restr0.0051445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.2410.36551600.3122515X-RAY DIFFRACTION96
3.241-3.41160.34681380.29982589X-RAY DIFFRACTION98
3.4116-3.6250.29651270.28322589X-RAY DIFFRACTION98
3.625-3.90430.36481190.26192559X-RAY DIFFRACTION96
3.9043-4.29620.30171210.24692451X-RAY DIFFRACTION92
4.2962-4.91530.25971510.22832560X-RAY DIFFRACTION96
4.9153-6.18330.30681390.2562463X-RAY DIFFRACTION92
6.1833-29.39680.2691330.22132509X-RAY DIFFRACTION92
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.2715-1.12450.11342.05572.10931.8637-0.18560.3399-0.3479-0.03750.6471-0.5874-0.34340.4572-0.28850.7605-0.07970.18850.8663-0.08820.938232.099814.8546-45.311
21.7256-0.23270.32055.3025-0.57950.8217-0.01070.35470.1576-0.1661-0.2145-0.91380.21660.19150.13450.5242-0.00970.12120.6669-0.03150.56517.468533.8688-48.8044
33.3193-0.7446-1.84875.1436-1.20782.55910.0253-0.09740.24270.74310.1674-0.0866-0.34950.0214-0.17760.3716-0.03840.01860.4556-0.01450.45374.722737.399-41.0586
42.8458-1.5051-1.0622.80810.43710.60120.313-0.2773-0.1330.68940.27171.5527-0.7881-0.0681-0.39170.99070.04960.33320.90860.23151.2298-14.567430.9851-31.101
54.49660.6092-1.32354.2974-2.25520.9395-0.21990.1041-0.0763-0.1660.42080.8660.4709-0.3928-0.09930.50310.01820.05850.6107-0.03660.5803-4.585927.6311-40.6678
64.77220.4651.42474.2257-1.30982.8726-0.0233-0.60630.1870.16030.0515-0.6293-0.14090.3762-0.06530.56540.0329-0.09670.71-0.05160.750532.657535.5578-28.6129
73.0776-0.35390.33382.5447-0.0780.10330.0715-0.38950.33270.3121-0.0899-0.74410.08150.1173-0.04620.790.0584-0.17730.5907-0.06980.582612.96878.15626.1542
84.4623-0.0987-0.57424.98520.47822.8979-0.1125-0.0271-0.2908-0.02280.04-0.3403-0.0730.24530.06020.5860.0306-0.06140.4305-0.0020.48380.9948-8.371-2.2336
92.4509-0.29181.72143.1008-1.61513.0377-0.17430.5741-0.0974-0.78220.43310.66830.28360.0406-0.2461.09750.0106-0.09930.76220.02680.6597-10.62750.9605-19.7457
101.9352-0.2378-0.40633.5022-1.69321.9465-0.0634-0.11750.1524-0.31040.37670.8504-0.6923-0.5615-0.07610.94180.0351-0.04520.5825-0.01080.6807-12.82913.4437-12.0324
114.7511-1.3725-0.08482.0305-0.5581.2625-0.32220.0802-0.131-0.40180.1621-0.58410.17960.43170.03020.932-0.03240.16010.7633-0.14720.82826.2209-2.9365-6.1502
129.8127-0.3222-5.64415.98450.23671.9665-2.54180.4766-1.21770.1303-0.8973-0.37360.52432.33092.55410.76120.2270.12041.32030.08981.429644.088913.3397-42.5946
13-0.0494-0.1296-0.13690.01220.0038-0.0424-0.1524-0.2929-0.28071.1551-0.6516-0.48430.36041.8136-01.5318-0.1402-0.3591.55920.15261.879532.397216.86513.0303
144.20142.48050.12425.67861.85742.4191-0.05270.15441.3742-0.0642-1.48310.7306-0.7952-0.20591.26921.1382-0.1513-0.2571.2915-0.00480.964829.390768.1771-29.9695
150.0588-0.1358-0.01390.63660.58370.4730.0899-0.5471.20630.6633-0.4734-0.4906-0.64040.837-0.25441.3818-0.3133-0.19791.20350.14771.330532.995265.9863-29.831
161.2578-1.61320.03792.1224-0.24625.21010.7243-0.83441.5187-0.48-0.88230.2352-0.08921.311-0.60840.8984-0.1863-0.56181.2471-0.23941.585539.655661.2162-29.7234
172.6024-2.23740.99762.3686-1.06692.79081.0190.2004-0.39410.3704-0.8056-2.5715-1.08750.92970.57830.7277-0.3032-0.28360.96-0.20831.672334.733158.0498-37.2538
180.6745-0.96340.27894.51980.38090.26490.19960.38050.2817-1.0772-0.4496-0.79530.3409-0.5930.56691.62380.2022-0.17611.0285-0.04321.443134.595270.7204-39.5919
191.81751.6325-1.0233.5276-0.16455.04760.58031.3779-0.11520.3659-0.6875-1.4244-0.7210.62740.21190.8255-0.1447-0.17521.05260.05390.841730.998554.5827-36.4393
202.0791-0.1316-1.01860.4945-2.63032.0187-1.74590.3007-1.8808-0.88090.6404-0.12160.4733-0.6341.66781.25210.2240.17611.54880.03711.139625.3532-35.5433-6.7395
212.20331.82810.33951.21041.36234.13490.41980.33940.1159-0.2468-0.4309-0.8666-1.34640.213-0.37471.03570.0870.44740.95540.0111.158228.47-34.2462-4.9283
223.2929-0.3282-1.7112.14911.82812.1380.1415-0.2253-0.38370.71320.6033-1.0724-1.12940.3752-0.54650.4180.30130.08471.44080.02481.117133.9679-29.6301-1.595
233.076-0.51970.48271.3375-0.95223.47750.5872-0.53560.65470.2968-0.7078-1.7797-0.4673-0.04680.47311.04920.2009-0.24011.0030.15961.803433.1856-21.5266-0.1723
241.35241.1221.97337.24470.73292.9821-0.239-0.1801-0.4428-0.1978-0.5874-1.61960.0908-0.44610.57381.05680.2717-0.16131.1857-0.19461.410222.2005-29.26633.8672
253.94171.00640.04075.84521.56951.2476-0.3521-0.4922-0.36890.7135-0.6249-0.891-0.0712-0.65590.60161.02550.0138-0.18971.2830.02791.270825.8255-37.45515.5813
264.836-1.5416-0.43835.9678-0.41944.23181.0791-0.8887-0.6514-0.1418-0.1750.3681-0.20121.6498-0.50330.65790.0611-0.02740.9478-0.16811.174723.5418-23.0862-0.0641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 383:429)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 430:511)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 512:575)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 576:625)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 626:695)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 696:806)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 384:473)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 474:557)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 558:632)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 633:680)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 681:806)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 105:112)
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 104:117)
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 1:6)
15X-RAY DIFFRACTION15CHAIN E AND (RESSEQ 7:22)
16X-RAY DIFFRACTION16CHAIN E AND (RESSEQ 23:34)
17X-RAY DIFFRACTION17CHAIN E AND (RESSEQ 35:49)
18X-RAY DIFFRACTION18CHAIN E AND (RESSEQ 50:64)
19X-RAY DIFFRACTION19CHAIN E AND (RESSEQ 65:75)
20X-RAY DIFFRACTION20CHAIN F AND (RESSEQ 1:7)
21X-RAY DIFFRACTION21CHAIN F AND (RESSEQ 8:22)
22X-RAY DIFFRACTION22CHAIN F AND (RESSEQ 23:34)
23X-RAY DIFFRACTION23CHAIN F AND (RESSEQ 35:40)
24X-RAY DIFFRACTION24CHAIN F AND (RESSEQ 41:49)
25X-RAY DIFFRACTION25CHAIN F AND (RESSEQ 50:64)
26X-RAY DIFFRACTION26CHAIN F AND (RESSEQ 65:75)

+
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