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- PDB-4hxd: Diversity of ubiquitin and ISG15 specificity amongst nairoviruses... -

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Basic information

Entry
Database: PDB / ID: 4hxd
TitleDiversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases
Components
  • Polyubiquitin-C
  • RNA-directed RNA polymerase L
Keywordshydrolase/viral protein / OTU-like Cysteine protease / Dugbe virus / deubiquitinase / 3-AMINOPROPANE / ubiquitin hydrolase / viral protein / hydrolase / ubiquitin. / hydrolase-viral protein complex
Function / homology
Function and homology information


cysteine-type deubiquitinase activity => GO:0004843 / RNA-templated viral transcription / negative stranded viral RNA replication / 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 ...cysteine-type deubiquitinase activity => GO:0004843 / RNA-templated viral transcription / negative stranded viral RNA replication / 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 / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Stabilization of p53 / EGFR downregulation / Negative regulation of FGFR1 signaling / Negative regulation of NOTCH4 signaling / Iron uptake and transport / G2/M Checkpoints
Similarity search - Function
Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Cathepsin B; Chain A / Zinc finger C2H2 type domain signature. ...Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Cathepsin B; Chain A / Zinc finger C2H2 type domain signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
1.7.6 3-bromanylpropan-1-amine / Polyubiquitin-C / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesHomo sapiens (human)
Dugbe virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsCapodagli, G.C. / Pegan, S.D.
CitationJournal: J.Virol. / Year: 2013
Title: Diversity of Ubiquitin and ISG15 Specificity among Nairoviruses' Viral Ovarian Tumor Domain Proteases.
Authors: Capodagli, G.C. / Deaton, M.K. / Baker, E.A. / Lumpkin, R.J. / Pegan, S.D.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Apr 3, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-C
B: RNA-directed RNA polymerase L
C: Polyubiquitin-C
D: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6279
Polymers57,0624
Non-polymers5645
Water82946
1
A: Polyubiquitin-C
B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7654
Polymers28,5312
Non-polymers2342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-19 kcal/mol
Surface area10790 Å2
MethodPISA
2
C: Polyubiquitin-C
D: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8615
Polymers28,5312
Non-polymers3303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-18 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.508, 39.991, 114.189
Angle α, β, γ (deg.)90.000, 97.330, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Polyubiquitin-C / Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pTyB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: P0CG48, ubiquitinyl hydrolase 1
#2: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase / Ubiquitin thioesterase / RNA- ...Protein L / Large structural protein / Replicase / Transcriptase / Ubiquitin thioesterase / RNA-directed RNA polymerase


Mass: 20011.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dugbe virus (isolate ArD44313) / Gene: L / Plasmid: pet11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q66431, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase
#3: Chemical ChemComp-4LJ / 1.7.6 3-bromanylpropan-1-amine


Mass: 138.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8BrN
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details3-AMINOPROPANE WAS COVALENTLY ADDED TO THE C-TERMINUS OF UBIQUITIN THROUGH USE OF INTERN CHEMISTRY ...3-AMINOPROPANE WAS COVALENTLY ADDED TO THE C-TERMINUS OF UBIQUITIN THROUGH USE OF INTERN CHEMISTRY BY COMPLEXING THE THIOESTERIFIED UBIQUITIN PROTEIN TOGETHER WITH 3-BROMOPROPYLAMINE AS PER WILKINSON, K. D., T. GAN-ERDENE, AND N. KOLLI. 2005. DERIVITIZATION OF THE C-TERMINUS OF UBIQUITIN AND UBIQUITIN-LIKE PROTEINS USING INTEIN CHEMISTRY: METHODS AND USES. METHODS ENZYMOL 399:37-51.

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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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.25 M LiSO4, 0.10 M Bis-Tris, 29% PEG 3350, 40% (v/v) 1,3-butanediol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 4, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 12408 / Num. obs: 11887 / % possible obs: 95.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.058 / Χ2: 0.958 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.85-2.92.90.1414860.686179
2.9-2.953.10.1335620.651198.1
2.95-3.013.20.1276270.667198.1
3.01-3.073.30.1165960.775197.9
3.07-3.143.20.1045960.762197.5
3.14-3.213.20.0975950.813198
3.21-3.293.20.096000.814198
3.29-3.383.20.086191.043197.3
3.38-3.483.20.0915801.777197.5
3.48-3.593.20.0746161.079197
3.59-3.723.20.0765731.686197
3.72-3.873.30.0655991.171197.1
3.87-4.043.30.0746152.057196.9
4.04-4.263.30.0525861.012196.9
4.26-4.523.40.0466080.89196.2
4.52-4.873.40.0425980.833196
4.87-5.363.40.0385890.636195.3
5.36-6.143.40.0366120.556195.5
6.14-7.733.30.0346060.551194.7
7.73-503.20.0356240.695192.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.83 Å48.02 Å
Translation2.83 Å48.02 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.817 / WRfactor Rfree: 0.2681 / WRfactor Rwork: 0.2044 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8047 / SU B: 18.255 / SU ML: 0.347 / SU Rfree: 0.4698 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.278 567 4.8 %RANDOM
Rwork0.2103 ---
obs0.2136 11868 95.16 %-
all-12472 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.61 Å2 / Biso mean: 20.821 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.02 Å2
2---0.23 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 23 46 3767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023792
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.965125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71824.629175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12515677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.771520
X-RAY DIFFRACTIONr_chiral_restr0.080.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212802
LS refinement shellResolution: 2.833→2.906 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 29 -
Rwork0.292 621 -
all-650 -
obs-621 75.23 %

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