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- PDB-4pij: X-ray crystal structure of the K11S/K63S double mutant of ubiquitin -

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Basic information

Entry
Database: PDB / ID: 4pij
TitleX-ray crystal structure of the K11S/K63S double mutant of ubiquitin
ComponentsUbiquitin
KeywordsPROTEIN BINDING / entropy-reduction / mutant
Function / homology
Function and homology information


Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression ...Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / APC-Cdc20 mediated degradation of Nek2A / cytosolic ribosome / 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 / Regulation of BACH1 activity / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, 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 / Degradation of DVL / 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 / Recognition of DNA damage by PCNA-containing replication complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / 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 / Degradation of GLI1 by the proteasome / Termination of translesion DNA synthesis / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of AXIN / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLoll, P.J. / Xu, P.J. / Schmidt, J. / Melideo, S.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Enhancing ubiquitin crystallization through surface-entropy reduction.
Authors: Loll, P.J. / Xu, P. / Schmidt, J.T. / Melideo, S.L.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)17,4448
Polymers16,8712
Non-polymers5726
Water1,45981
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5282
Polymers8,4361
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9166
Polymers8,4361
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-87 kcal/mol
Surface area7650 Å2
MethodPISA
4
B: Ubiquitin
hetero molecules

A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4448
Polymers16,8712
Non-polymers5726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2030 Å2
ΔGint-79 kcal/mol
Surface area8060 Å2
MethodPISA
5
B: Ubiquitin
hetero molecules

A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4448
Polymers16,8712
Non-polymers5726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area1810 Å2
ΔGint-74 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.970, 48.850, 80.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is one monomer; there are two biological units in the asymmetric unit (chains A & B)

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Components

#1: Protein Ubiquitin /


Mass: 8435.574 Da / Num. of mol.: 2 / Mutation: K11S, K63S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSETA / Cell line (production host): Rosetta2(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P62987
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 1.86 Å3/Da / Density % sol: 33.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.2M ammonium sulfate, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 20416 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 13.38 Å2 / Rmerge F obs: 0.055 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.049 / Χ2: 0.996 / Net I/σ(I): 21.78 / Num. measured all: 121636
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.543.80.2880.2524.34830152612540.29182.2
1.54-1.580.2330.2245.085845146513630.25493
1.58-1.630.1960.2186.217602144614280.24298.8
1.63-1.680.1610.2057.598896139913980.22399.9
1.68-1.730.1340.1738.948703132413230.18899.9
1.73-1.790.1010.14110.798430131013090.15499.9
1.79-1.860.0850.11712.918048127512740.12899.9
1.86-1.940.0660.09416.727957122412240.102100
1.94-2.020.050.07420.467779119111890.0899.8
2.02-2.120.0460.06823.647233112711260.07499.9
2.12-2.240.0390.05726.336658107510730.06399.8
2.24-2.370.0330.05229.356371100710060.05699.9
2.37-2.540.0290.04931.862669679660.05399.9
2.54-2.740.0260.04334.9556229008990.04799.9
2.74-30.0240.03739.5850358368340.0499.8
3-3.350.020.03246.5848107597560.03599.6
3.35-3.870.0160.02753.6440586766750.0399.9
3.87-4.740.0130.02258.3333175895840.02499.2
4.74-6.710.0140.02455.0927384674630.02699.1
6.710.0140.02255.5814382802720.02597.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
X-PLORrefinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H7P
Resolution: 1.5→24.425 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 2000 9.8 %
Rwork0.1759 --
obs0.1781 20414 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.5→24.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 31 83 1296
Biso mean--25.94 29.69 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071233
X-RAY DIFFRACTIONf_angle_d1.1511669
X-RAY DIFFRACTIONf_dihedral_angle_d15.022478
X-RAY DIFFRACTIONf_chiral_restr0.074198
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.53760.23341180.19641081X-RAY DIFFRACTION82
1.5376-1.57920.22331330.19361230X-RAY DIFFRACTION93
1.5792-1.62560.22111410.18831296X-RAY DIFFRACTION99
1.6256-1.67810.24521430.1891316X-RAY DIFFRACTION100
1.6781-1.7380.20031420.17841316X-RAY DIFFRACTION100
1.738-1.80760.19511440.18241321X-RAY DIFFRACTION100
1.8076-1.88990.21321460.1661344X-RAY DIFFRACTION100
1.8899-1.98940.18871420.16261308X-RAY DIFFRACTION100
1.9894-2.1140.17831460.1551341X-RAY DIFFRACTION100
2.114-2.27710.18471450.16521333X-RAY DIFFRACTION100
2.2771-2.50610.19761450.17291344X-RAY DIFFRACTION100
2.5061-2.86820.20611480.17151358X-RAY DIFFRACTION100
2.8682-3.61180.19811500.16771378X-RAY DIFFRACTION100
3.6118-24.42820.18861570.1921448X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2395-0.2335-0.55821.83290.2731.38670.02550.08680.0806-0.0857-0.054-0.0563-0.0597-0.12170.02970.08540.0021-0.01250.0823-0.0110.0856-1.0899-16.443710.2686
22.066-0.06990.47151.1950.38691.3519-0.0337-0.0963-0.04250.04150.00350.1009-0.0122-0.07160.03180.08140.00080.00720.0962-0.00150.0778-14.2438-34.36959.9142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 75
2X-RAY DIFFRACTION2chain BB1 - 75

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