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- PDB-5god: Lys27-linked di-ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5god
TitleLys27-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 / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator ...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 / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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) / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / cytosolic ribosome / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / neuron projection morphogenesis / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / 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 / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / 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: 1.15 Å
AuthorsGao, S. / Pan, M. / Zheng, Y.
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_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: D-ubiquitin
D: D-ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2815
Polymers34,2574
Non-polymers241
Water6,125340
1
A: Ubiquitin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1783
Polymers17,1542
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: D-ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,5521
Polymers8,5521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: 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)38.240, 38.260, 48.000
Angle α, β, γ (deg.)98.15, 98.15, 109.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ubiquitin


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


Mass: 8551.744 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62987*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 1.88 Å3/Da / Density % sol: 34.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate trihydrate PH6.5, 20% PEG 8000

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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: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.15→35.275 Å / Num. obs: 67808 / % possible obs: 77 % / Redundancy: 1.93 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 11.42
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.604

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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: 1.15→35.275 Å / SU ML: 0.11 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 26.51
RfactorNum. reflection% reflection
Rfree0.2215 3287 4.85 %
Rwork0.2021 --
obs0.2031 67778 76.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.15→35.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 1 340 2745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062429
X-RAY DIFFRACTIONf_angle_d0.983264
X-RAY DIFFRACTIONf_dihedral_angle_d22.081960
X-RAY DIFFRACTIONf_chiral_restr0.077388
X-RAY DIFFRACTIONf_plane_restr0.006420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1495-1.16670.3062410.3216661X-RAY DIFFRACTION18
1.1667-1.18490.3251590.311991X-RAY DIFFRACTION27
1.1849-1.20430.3193530.31378X-RAY DIFFRACTION37
1.2043-1.22510.2347700.28531860X-RAY DIFFRACTION50
1.2251-1.24740.28911230.28862572X-RAY DIFFRACTION71
1.2474-1.27140.3081600.26522903X-RAY DIFFRACTION79
1.2714-1.29730.31341490.27073169X-RAY DIFFRACTION86
1.2973-1.32550.25881750.25663074X-RAY DIFFRACTION85
1.3255-1.35640.2711650.24822912X-RAY DIFFRACTION80
1.3564-1.39030.25611420.24513147X-RAY DIFFRACTION86
1.3903-1.42790.24811780.22193216X-RAY DIFFRACTION88
1.4279-1.46990.22991740.21523188X-RAY DIFFRACTION87
1.4699-1.51730.19741600.20893135X-RAY DIFFRACTION87
1.5173-1.57160.23071630.20183074X-RAY DIFFRACTION83
1.5716-1.63450.25991370.19723095X-RAY DIFFRACTION84
1.6345-1.70890.22051800.19663228X-RAY DIFFRACTION90
1.7089-1.7990.20041580.19493263X-RAY DIFFRACTION89
1.799-1.91170.18941570.19713309X-RAY DIFFRACTION88
1.9117-2.05920.21371670.1863045X-RAY DIFFRACTION85
2.0592-2.26640.22441790.18693406X-RAY DIFFRACTION93
2.2664-2.59430.22011710.19813302X-RAY DIFFRACTION90
2.5943-3.26820.21941530.19743210X-RAY DIFFRACTION88
3.2682-35.29180.19421730.183353X-RAY DIFFRACTION92

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