PDB-2ru6: The pure alternative state of ubiquitin

Basic information

• Entry: Database: PDB / ID: 2ru6
• Title: The pure alternative state of ubiquitin
• Components: Ubiquitin
• Keywords: PROTEIN BINDING / ubiquitin / alternatively folded state / high-pressure NMR / Q41N variant

Function / homology

Function:

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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR2 signaling / Degradation of DVL / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis / Degradation of AXIN / Hh mutants are degraded by ERAD / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Activation of NF-kappaB in B cells / Iron uptake and transport / Recognition of DNA damage by PCNA-containing replication complex / Assembly Of The HIV Virion / Degradation of GLI1 by the proteasome / Spry regulation of FGF signaling / Hedgehog ligand biogenesis

Domain/homology:

: / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily

Component:

Polyubiquitin-C

• Biological species: Homo sapiens (human)
• Method: SOLUTION NMR / torsion angle dynamics, Energy minimization
• Model details: lowest energy, model1
• Authors: Kitazawa, S. / Kameda, T. / Kumo, A. / Utsumi, M. / Baxter, N. / Kato, K. / Williamson, M.P. / Kitahara, R.
• Citation: Journal: Biochemistry / Year: 2014; Title: Close Identity between Alternatively Folded State N2 of Ubiquitin and the Conformation of the Protein Bound to the Ubiquitin-Activating Enzyme; Authors: Kitazawa, S. / Kameda, T. / Kumo, A. / Yagi-Utsumi, M. / Baxter, N.J. / Kato, K. / Williamson, M.P. / Kitahara, R.

History

Deposition	Dec 4, 2013	Deposition site: BMRB / Processing site: PDBJ
Revision 1.0	Feb 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 5, 2014	Group: Structure summary
Revision 1.2	Jun 14, 2023	Group: Data collection / Database references / Other Category: database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3	May 15, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

Assembly

Deposited unit

A: Ubiquitin

Summary:

• 8.56 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,563	1
Polymers	8,563	1
Non-polymers	0	0
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	20 / 200	structures with the lowest energy
Representative	Model #1	lowest energy

Components

#1: Protein

A Ubiquitin

Details:

Mass: 8562.805 Da / Num. of mol.: 1 / Mutation: Q41N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48

Experimental details

Experiment

• Experiment: Method: SOLUTION NMR

NMR experiment

Conditions-ID	Experiment-ID	Solution-ID	Type
1	1	1	2D 1H-15N HSQC
1	2	1	2D 1H-13C HSQC aliphatic
1	3	1	2D 1H-13C HSQC aromatic
1	4	1	2D HNCO
1	5	1	3D 1H-13C/15N simultaneous evolutio NOESY HSQC

Sample preparation

• Details: Contents: 20 mM [U-100% 2H] Tris(hydroxymethyl)aminomethane-1, 2 mM [U-100% 13C; U-100% 15N] ubiquitin-2, 0.2 mM DSS-3, 88% H2O/12% D2O; Solvent system: 88% H2O/12% D2O

Sample

Conc. (mg/ml)	Component	Isotopic labeling	Solution-ID
20 mM	Tris(hydroxymethyl)aminomethane-1	[U-100% 2H]	1
2 mM	ubiquitin-2	[U-100% 13C; U-100% 15N]	1
0.2 mM	DSS-3		1

• Sample conditions: Ionic strength: 20 / pH: 7.2 / Pressure: 250 0 / Temperature: 298 K

NMR measurement

• NMR spectrometer: Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

Processing

NMR software

Name	Version	Developer	Classification
CYANA	3.93	Guntert, Mumenthaler and Wuthrich	chemical shift assignment
Amber	11	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman	refinement
NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax	processing
NMRView		Johnson, One Moon Scientific	peak picking
CYANA_3.93			refinement

• Refinement: Method: torsion angle dynamics, Energy minimization / Software ordinal: 1
• NMR constraints: NOE constraints total: 2450 / NOE intraresidue total count: 0 / NOE long range total count: 454 / NOE medium range total count: 231 / NOE sequential total count: 1765 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 36 / Protein psi angle constraints total count: 36
• NMR representative: Selection criteria: lowest energy
• NMR ensemble: Conformer selection criteria: structures with the lowest energy; Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1