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- PDB-7s6o: The crystal structure of Lys48-linked di-ubiquitin -

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Basic information

Entry
Database: PDB / ID: 7s6o
TitleThe crystal structure of Lys48-linked di-ubiquitin
Components(Ubiquitin) x 2
KeywordsSIGNALING PROTEIN / ubiquitin / di-ubiquitin
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / positive regulation of protein ubiquitination / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Deactivation of the beta-catenin transactivating complex / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling
Similarity search - Function
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 ...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
Similarity search - Domain/homology
ACETATE ION / Polyubiquitin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsOsipiuk, J. / Tesar, C. / Lanham, B.T. / Wydorski, P. / Fushman, D. / Joachimiak, L. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nat Commun / Year: 2023
Title: Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.
Authors: Wydorski, P.M. / Osipiuk, J. / Lanham, B.T. / Tesar, C. / Endres, M. / Engle, E. / Jedrzejczak, R. / Mullapudi, V. / Michalska, K. / Fidelis, K. / Fushman, D. / Joachimiak, A. / Joachimiak, L.A.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Author supporting evidence / Structure summary
Category: audit_author / pdbx_audit_support / struct_keywords
Item: _struct_keywords.text
Revision 2.0Mar 16, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_database_related / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_ref_seq_dif / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns.d_resolution_low / _reflns.pdbx_CC_half / _reflns.pdbx_CC_star / _reflns.pdbx_netI_over_av_sigmaI / _reflns.pdbx_number_measured_all / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_CC_star / _software.classification / _software.name / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_label_comp_id
Description: Model orientation/position
Details: The previous deposition based on small differences in electron density maps and had wrong assignment of chains due to invisibility of linker between molecules. We were informed about similar ...Details: The previous deposition based on small differences in electron density maps and had wrong assignment of chains due to invisibility of linker between molecules. We were informed about similar structure at lower resolution which had visible linker. The swap of chains was necessary to get proper chain order.
Provider: author / Type: Coordinate replacement
Revision 2.1May 31, 2023Group: 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
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4154
Polymers17,2972
Non-polymers1182
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint2 kcal/mol
Surface area8000 Å2
Unit cell
Length a, b, c (Å)23.804, 56.577, 46.201
Angle α, β, γ (deg.)90.000, 93.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin


Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K48R
Source method: isolated from a genetically manipulated source
Details: GLY76 of chain A is connected by the isopeptide bond to epsilon amino group of LYS48 of chain B. The isopeptide linkage was not resolved in the structure.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0CG47
#2: Protein Ubiquitin


Mass: 8691.918 Da / Num. of mol.: 1 / Mutation: Aspartic acid residue added to C terminus (D77)
Source method: isolated from a genetically manipulated source
Details: GLY76 of chain A is connected by the isopeptide bond to epsilon amino group of LYS48 of chain B. The isopeptide linkage was not resolved in the structure.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0CG47
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
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: 1.8 Å3/Da / Density % sol: 31.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 50 mM acetate, 8.6% PEG2000 MME, 17.1% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 28558 / % possible obs: 84.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Χ2: 1.671 / Net I/σ(I): 10.9 / Num. measured all: 91217
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.25-1.272.10.4975760.6240.4240.6561.10734.9
1.27-1.292.20.4737140.6270.3860.6131.05143
1.29-1.322.40.458980.7060.3550.5760.92452.6
1.32-1.352.50.4229820.7090.3260.5371.07260.2
1.35-1.382.70.3612290.8280.2710.4531.05872.8
1.38-1.4130.33915550.8580.2320.4131.15490.7
1.41-1.443.20.28615650.9070.1850.3411.28694.5
1.44-1.483.20.25615950.9080.1650.3061.37793.9
1.48-1.533.30.19715820.9530.1270.2351.60595.1
1.53-1.573.20.17215600.9520.1130.2061.74692.4
1.57-1.633.50.1515810.9670.0930.1771.75795.4
1.63-1.73.50.13716660.9730.0850.1621.89196.1
1.7-1.773.40.12415990.9740.0790.1481.90496.8
1.77-1.873.20.10215720.9780.0660.1221.93593.7
1.87-1.983.50.09216490.9850.0560.1081.91496.7
1.98-2.143.50.08616390.9870.0530.1011.87796.9
2.14-2.353.30.07816320.9870.0510.0941.83695.8
2.35-2.693.50.07516410.9880.0460.0881.9297.2
2.69-3.393.40.06416580.990.0410.0761.89497.1
3.39-503.50.05616650.9910.0350.0661.78496.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5E6J

5e6j


Resolution: 1.25→46.12 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.922 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 1363 4.8 %RANDOM
Rwork0.1292 ---
obs0.1313 27176 84.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.22 Å2 / Biso mean: 17.608 Å2 / Biso min: 9.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20.07 Å2
2---1.07 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.25→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 8 141 1330
Biso mean--32.77 33.38 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151382
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6581800
X-RAY DIFFRACTIONr_angle_other_deg1.3321.5933212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2755178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.89523.23971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84715287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0591510
X-RAY DIFFRACTIONr_chiral_restr0.080.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02278
X-RAY DIFFRACTIONr_rigid_bond_restr1.43432701
LS refinement shellResolution: 1.25→1.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 44 -
Rwork0.269 819 -
all-863 -
obs--35.1 %

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