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- PDB-6ypt: X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex ... -

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Basic information

Entry
Database: PDB / ID: 6ypt
TitleX-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin
Components
  • Polyubiquitin-C
  • RNA replicase polyprotein
KeywordsVIRAL PROTEIN / PRO/DUB / Deubiquitinase / TYMV / Ubiquitin
Function / homology
Function and homology information


mRNA methyltransferase activity / RNA processing / 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 ...mRNA methyltransferase activity / RNA processing / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / 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 / Transferases; Transferring one-carbon groups; Methyltransferases / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / 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 / Peroxisomal protein import / Termination of translesion DNA synthesis / 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
Peptidase family C21 domain profile. / Peptidase C21 / Tymovirus endopeptidase domain / Salyut domain / Tymovirus endopeptidase / Salyut domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase ...Peptidase family C21 domain profile. / Peptidase C21 / Tymovirus endopeptidase domain / Salyut domain / Tymovirus endopeptidase / Salyut domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Ubiquitin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
METHYL 4-AMINOBUTANOATE / Polyubiquitin-C / RNA replicase polyprotein
Similarity search - Component
Biological speciesTurnip yellow mosaic virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.663 Å
AuthorsFieulaine, S. / Bressanelli, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency11-BSV8-011 France
CitationJournal: J.Biol.Chem. / Year: 2020
Title: X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin
Authors: Fieulaine, S. / Bressanelli, S.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 15, 2023Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 3.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA replicase polyprotein
B: Polyubiquitin-C
C: RNA replicase polyprotein
D: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2626
Polymers55,0284
Non-polymers2342
Water0
1
A: RNA replicase polyprotein
B: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6313
Polymers27,5142
Non-polymers1171
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-9 kcal/mol
Surface area10760 Å2
MethodPISA
2
C: RNA replicase polyprotein
D: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6313
Polymers27,5142
Non-polymers1171
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-9 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.930, 51.860, 125.250
Angle α, β, γ (deg.)90.000, 98.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEUchain AAA732 - 87613 - 157
21LEULEULEULEUchain CCC732 - 87613 - 157
12METMETGLYGLYchain BBB1 - 7511 - 85
22METMETGLYGLYchain DDD1 - 7511 - 85

NCS ensembles :
ID
1
2

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Components

#1: Protein RNA replicase polyprotein / 206 kDa polyprotein


Mass: 17778.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turnip yellow mosaic virus / Production host: Escherichia coli (E. coli)
References: UniProt: P10358, Transferases; Transferring one-carbon groups; Methyltransferases, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Hydrolases; Acting on acid ...References: UniProt: P10358, Transferases; Transferring one-carbon groups; Methyltransferases, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, RNA-directed RNA polymerase
#2: Protein Polyubiquitin-C


Mass: 9735.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Chemical ChemComp-GVE / METHYL 4-AMINOBUTANOATE


Type: peptide-like / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 21% PEG-20K + 0.1M MES-NaOH pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.66→37.46 Å / Num. obs: 5303 / % possible obs: 97 % / Redundancy: 3.3 % / Biso Wilson estimate: 106.53 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.215 / Net I/σ(I): 4.14
Reflection shellResolution: 3.663→3.81 Å / Redundancy: 3.3 % / Num. unique obs: 715 / CC1/2: 0.415 / % possible all: 83.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LW5

5lw5


Resolution: 3.663→37.46 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.54
RfactorNum. reflection% reflection
Rfree0.2827 265 5.01 %
Rwork0.2057 --
obs0.2094 5291 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 435.15 Å2 / Biso mean: 175.6872 Å2 / Biso min: 46.98 Å2
Refinement stepCycle: final / Resolution: 3.663→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 16 0 3480
Biso mean--190.88 --
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033558
X-RAY DIFFRACTIONf_angle_d0.4954852
X-RAY DIFFRACTIONf_chiral_restr0.038570
X-RAY DIFFRACTIONf_plane_restr0.004632
X-RAY DIFFRACTIONf_dihedral_angle_d12.8522192
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1414X-RAY DIFFRACTION0.243TORSIONAL
12C1414X-RAY DIFFRACTION0.243TORSIONAL
21B766X-RAY DIFFRACTION0.243TORSIONAL
22D766X-RAY DIFFRACTION0.243TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.663-4.61360.32111280.2394241594
4.6136-37.460.26381370.1889261199
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)
10.2868-0.18970.09713.6038-0.31531.40360.0982-0.06260.0806-0.1355-0.01120.3890.2886-0.12350.09830.5027-0.0499-0.01020.1444-0.1521.2075-14.4923-12.4697-51.2925
20.98291.33080.14956.0524-1.12124.7599-0.3583-0.29440.8940.2330.2383-0.8328-0.73070.19570.02760.58450.0202-0.15060.4532-0.18531.3893-28.86122.7203-42.2872
32.3708-0.1764-0.61954.9631.34072.8508-1.1098-2.9864-0.40460.96950.86910.00351.01570.5621-0.07611.77780.66430.18453.38980.10931.5761-13.88-18.9602-11.3285
41.31850.09160.28145.95190.95952.6055-0.1232-0.7193-0.21520.19080.4533-0.9007-1.97360.95920.2122.2304-0.36170.10793.6073-0.73592.32870.0935-1.3182-16.1132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' )A0
2X-RAY DIFFRACTION2(chain 'B' )B0
3X-RAY DIFFRACTION3(chain 'C' )C0
4X-RAY DIFFRACTION4(chain 'D' )D0

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