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- PDB-7jms: Structure of the Hazara virus OTU bound to ubiquitin -

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Basic information

Entry
Database: PDB / ID: 7jms
TitleStructure of the Hazara virus OTU bound to ubiquitin
Components
  • Polyubiquitin-B
  • ReplicaseRNA-dependent RNA polymerase
KeywordsHYDROLASE / DUB / OTU
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of proteasomal protein catabolic process ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / 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 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / 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
Similarity search - Function
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. / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain ...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. / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Replicase / Polyubiquitin-B
Similarity search - Component
Biological speciesHazara orthonairovirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsDzimianski, J.V. / Pegan, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI109008 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Flipping the substrate preference of Hazara virus ovarian tumour domain protease through structure-based mutagenesis.
Authors: Dzimianski, J.V. / Mace, S.L. / Williams, I.L. / Freitas, B.T. / Pegan, S.D.
History
DepositionAug 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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
A: Replicase
B: Polyubiquitin-B
C: Replicase
D: Polyubiquitin-B
E: Replicase
F: Polyubiquitin-B
G: Replicase
H: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,92123
Polymers114,1488
Non-polymers77315
Water4,864270
1
A: Replicase
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8067
Polymers28,5372
Non-polymers2695
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-35 kcal/mol
Surface area11120 Å2
MethodPISA
2
C: Replicase
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8067
Polymers28,5372
Non-polymers2695
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-20 kcal/mol
Surface area11200 Å2
MethodPISA
3
E: Replicase
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6745
Polymers28,5372
Non-polymers1373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-13 kcal/mol
Surface area10920 Å2
MethodPISA
4
G: Replicase
H: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6344
Polymers28,5372
Non-polymers972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-21 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.850, 55.595, 97.434
Angle α, β, γ (deg.)90.000, 97.203, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Replicase / RNA-dependent RNA polymerase / Transcriptase


Mass: 20017.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hazara orthonairovirus / Production host: Escherichia coli (E. coli)
References: UniProt: A6XA53, RNA-directed RNA polymerase, ubiquitinyl hydrolase 1
#2: Protein
Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 4 types, 285 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE / Allylamine


Mass: 57.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7N
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.3 M calcium chloride, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 22676 / % possible obs: 96.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 47.15 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.84
Reflection shellResolution: 2.78→2.83 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1993 / CC1/2: 0.641

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PRP, 4HXD, 5JZE, 6OAR

3prp

4hxd

5jze

6oar


Resolution: 2.78→41.59 Å / SU ML: 0.426 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0515
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2731 1082 4.91 %
Rwork0.2348 20970 -
obs0.2367 22052 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.34 Å2
Refinement stepCycle: LAST / Resolution: 2.78→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7361 0 37 270 7668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00597565
X-RAY DIFFRACTIONf_angle_d0.950210238
X-RAY DIFFRACTIONf_chiral_restr0.06171164
X-RAY DIFFRACTIONf_plane_restr0.00521317
X-RAY DIFFRACTIONf_dihedral_angle_d22.49962796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.910.35421390.3032594X-RAY DIFFRACTION98.34
2.91-3.060.33341410.27342637X-RAY DIFFRACTION98.76
3.06-3.250.34471360.24792653X-RAY DIFFRACTION98.2
3.25-3.50.28081340.2332608X-RAY DIFFRACTION97.06
3.5-3.850.25331380.21532577X-RAY DIFFRACTION96.38
3.85-4.410.23311320.20462599X-RAY DIFFRACTION95.89
4.41-5.560.23461340.21252633X-RAY DIFFRACTION96.18
5.56-41.590.27721280.25632669X-RAY DIFFRACTION95.04

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