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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


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Tail fiber
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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