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- PDB-5gob: Lys6-linked di-ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5gob
TitleLys6-linked di-ubiquitin
Components
  • D-ubiquitin
  • Ubiquitin
KeywordsPROTEIN BINDING / polyubiquitin chains / quasi-racemic crystal
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 / Peptide chain elongation / Selenocysteine synthesis ...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 / 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 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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) / 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 / 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 / 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 / cytosolic ribosome / 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 / regulation of mitochondrial membrane potential / 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 / 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 / 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
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e 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
polypeptide(D) / polypeptide(D) (> 10) / Polyubiquitin-B / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.153 Å
AuthorsGao, S. / Pan, M. / Zheng, Y. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China2013CB932800 China
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Monomer/Oligomer Quasi-Racemic Protein Crystallography
Authors: Gao, S. / Pan, M. / Zheng, Y. / Huang, Y. / Zheng, Q. / Sun, D. / Lu, L. / Tan, X. / Tan, X. / Lan, H. / Wang, J. / Wang, T. / Wang, J. / Liu, L.
History
DepositionJul 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Feb 9, 2022Group: Database references / Derived calculations / Category: database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin
B: D-ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1292
Polymers17,1292
Non-polymers00
Water3,441191
1
A: Ubiquitin

A: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1542
Polymers17,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
2
B: D-ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,5521
Polymers8,5521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.730, 26.380, 45.120
Angle α, β, γ (deg.)98.07, 93.85, 106.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47
#2: Protein D-ubiquitin


Mass: 8551.744 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62987*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.62 Å3/Da / Density % sol: 24.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2M Magnesium chloride hexahydrate, 20% PEG 3350, PH5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.153→44.39 Å / Num. obs: 23485 / % possible obs: 62 % / Redundancy: 3.54 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.25
Reflection shellResolution: 1.16→1.2 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.749

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Processing

SoftwareName: PHENIX / Version: (1.10.1_2155: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 1.153→44.388 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 35.93
RfactorNum. reflection% reflection
Rfree0.2285 1207 5.15 %
Rwork0.1912 --
obs0.1931 23459 61.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.153→44.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 0 191 1385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051206
X-RAY DIFFRACTIONf_angle_d1.0141622
X-RAY DIFFRACTIONf_dihedral_angle_d19.345478
X-RAY DIFFRACTIONf_chiral_restr0.079194
X-RAY DIFFRACTIONf_plane_restr0.004208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1528-1.1990.423760.2771131X-RAY DIFFRACTION3
1.199-1.25350.3836330.2789569X-RAY DIFFRACTION14
1.2535-1.31960.2869800.24041289X-RAY DIFFRACTION32
1.3196-1.40230.28661370.23432173X-RAY DIFFRACTION56
1.4023-1.51060.27851830.20533562X-RAY DIFFRACTION89
1.5106-1.66260.24441970.18233597X-RAY DIFFRACTION90
1.6626-1.90320.23962260.18013550X-RAY DIFFRACTION89
1.9032-2.39780.17671930.18733653X-RAY DIFFRACTION92
2.3978-44.42070.22361520.18733728X-RAY DIFFRACTION92

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