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- PDB-5goi: Lys48-linked di-ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5goi
TitleLys48-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 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation ...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 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / energy homeostasis / regulation of neuron apoptotic process / 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 / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / 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 / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / 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 / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / neuron projection morphogenesis / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / 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 domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. ...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: 1.594 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 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr2_symmetry
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


Theoretical massNumber of molelcules
Total (without water)34,2574
Polymers34,2574
Non-polymers00
Water3,981221
1
A: Ubiquitin
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1542
Polymers17,1542
Non-polymers00
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)28.010, 40.800, 52.160
Angle α, β, γ (deg.)98.45, 100.90, 105.94
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.61 Å3/Da / Density % sol: 23.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium citrate tribasic dehydrate PH5.6, 20% 2-Propanol, 20%PEG 4000

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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: 1.594→38.351 Å / Num. obs: 23441 / % possible obs: 82 % / Redundancy: 1.69 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 4
Reflection shellResolution: 1.59→1.64 Å / Redundancy: 1.62 % / Rmerge(I) obs: 1.086

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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: 1.594→38.351 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 40.66
RfactorNum. reflection% reflection
Rfree0.3106 1134 4.84 %
Rwork0.2642 --
obs0.2665 23422 82.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.594→38.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 0 221 2625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042432
X-RAY DIFFRACTIONf_angle_d0.7833271
X-RAY DIFFRACTIONf_dihedral_angle_d18.2791245
X-RAY DIFFRACTIONf_chiral_restr0.053389
X-RAY DIFFRACTIONf_plane_restr0.003421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5935-1.66610.3693780.34441379X-RAY DIFFRACTION41
1.6661-1.75390.3553930.35191990X-RAY DIFFRACTION58
1.7539-1.86380.37271610.32273143X-RAY DIFFRACTION92
1.8638-2.00770.34561540.31073168X-RAY DIFFRACTION95
2.0077-2.20970.33061710.2813179X-RAY DIFFRACTION94
2.2097-2.52940.33691580.27243196X-RAY DIFFRACTION94
2.5294-3.18650.32931730.26323141X-RAY DIFFRACTION93
3.1865-38.36220.25521460.2213092X-RAY DIFFRACTION91
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0719-0.02240.08890.0079-0.02820.11320.1243-0.03990.1131-0.01310.056-0.0048-0.07740.00130.08230.2981-0.05090.12540.1714-0.05670.2282-11.2697.852421.0567
20.0008-0.0035-0.00570.0210.03520.07520.1124-0.0231-0.00710.0640.0035-0.1359-0.0310.01840.01430.2026-0.03280.01510.2290.00250.2209-0.15249.545822.5753
30.0181-0.0061-0.01630.01990.0060.0039-0.0066-0.0480.0561-0.0325-0.108-0.05440.1017-0.0324-00.19880.03460.04510.22630.03650.1545-0.21142.837615.8387
40.02890.02970.00480.0284-0.00950.01850.0590.04180.0273-0.0215-0.05850.0612-0.08170.0517-0.01770.34220.04380.09260.17640.03860.1865-6.38819.54713.3365
50.03330.0447-0.01720.0668-0.01520.0155-0.01470.02790.0296-0.04480.0050.0203-0.0084-0.0382-0.00040.10710.00620.03880.23930.03440.23942.4556-9.803120.605
60.04670.0309-0.0910.0191-0.05920.21770.0566-0.0214-0.00780.0110.1603-0.15390.0319-0.13970.02420.2772-0.0096-0.02570.16740.01340.230317.7447-5.24993.7904
70.00390.0099-0.0020.0302-0.00590.0009-0.0039-0.0134-0.0241-0.0023-0.00620.03040.0075-0.0314-0.01040.05820.1220.0040.32890.08260.19943.2887-4.61646.6317
80.01190.00790.01410.03270.02950.0271-0.03010.12870.0528-0.0347-0.00320.00450.0071-0.039-0.03970.17380.0095-0.08150.1648-0.02880.202311.2687-14.67741.294
90.0885-0.0161-0.02740.03930.02540.0208-0.0142-0.0306-0.05920.0662-0.02590.01590.01070.0407-0.06730.1161-0.0603-0.05830.22860.02760.17529.0223-12.822113.7959
100.0103-0.0030.00490.00360.00120.0120.019-0.0258-0.03430.00290.03350.0147-0.0352-0.0153-0.00210.0352-0.0533-0.05120.24040.04980.17979.4874-2.692513.4164
110.0939-0.01730.06290.0158-0.03380.1002-0.07250.02940.00590.0045-0.03420.0230.0172-0.0683-0.07970.1827-0.01020.00010.1817-0.02640.158516.9601-18.74256.2328
120.18190.120.06210.14930.01890.0508-0.00520.0726-0.1542-0.05860.0765-0.2171-0.0768-0.05220.07960.31050.22680.2626-0.1547-0.2854-0.1285-11.397311.4625-6.5215
130.17380.035-0.00890.048-0.00920.0146-0.02110.0837-0.11370.04220.0933-0.02450.0882-0.08870.01530.2163-0.00510.02610.1203-0.01910.1622.5128-5.8367-18.1573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 56 )
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 76 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 16 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 22 )
8X-RAY DIFFRACTION8chain 'B' and (resid 23 through 44 )
9X-RAY DIFFRACTION9chain 'B' and (resid 45 through 56 )
10X-RAY DIFFRACTION10chain 'B' and (resid 57 through 65 )
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 76 )
12X-RAY DIFFRACTION12chain 'C' and (resid 10 through 76 )
13X-RAY DIFFRACTION13chain 'D' and (resid 10 through 76 )

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