PDB-2mbq: K11-linked Diubiquitin average solution structure at pH 6.8, 150 ...

Basic information

• Entry: Database: PDB / ID: 2mbq
• Title: K11-linked Diubiquitin average solution structure at pH 6.8, 150 mM NaCl
• Components: Ubiquitin
• Keywords: SIGNALING PROTEIN / diubiquitin / K11

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 / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Downregulation of ERBB2:ERBB3 signaling / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / 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 / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Regulation of signaling by CBL / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ubiquitin-dependent degradation of Cyclin D / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Fanconi Anemia Pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulation of FGFR3 signaling / Peroxisomal protein import / TNFR2 non-canonical NF-kB pathway / Deactivation of the beta-catenin transactivating complex / Stabilization of p53 / Assembly of the pre-replicative complex / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Vpu mediated degradation of CD4 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR1 signaling / Termination of translesion DNA synthesis / EGFR downregulation / Regulation of TNFR1 signaling / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Assembly Of The HIV Virion / Degradation of CRY and PER proteins / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Spry regulation of FGF signaling / Iron uptake and transport / Late endosomal microautophagy / Degradation of GLI1 by the proteasome

Domain/homology:

Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta

Component:

Polyubiquitin-C

• Biological species: Homo sapiens (human)
• Method: SOLUTION NMR / in-house RDC (orientation), MTSL (distance)
• Model details: closest to the average, model1
• Authors: Castaneda, C.A. / Fushman, D.
• Citation: Journal: Structure / Year: 2013; Title: Unique structural, dynamical, and functional properties of k11-linked polyubiquitin chains.; Authors: Castaneda, C.A. / Kashyap, T.R. / Nakasone, M.A. / Krueger, S. / Fushman, D.

History

Deposition	Aug 3, 2013	Deposition site: BMRB / Processing site: RCSB
Revision 1.0	Sep 4, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jun 14, 2023	Group: Data collection / Database references / Other Category: database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer 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
Revision 1.2	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

B: Ubiquitin

Summary:

• 17.2 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	17,154	2
Polymers	17,154	2
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)	1 / 1	target function
Representative	Model #1	closest to the average

Components

#1: Protein

A B Ubiquitin

Details:

Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pJY2 / References: UniProt: P0CG48

• Sequence details: DISTAL UBIQUITIN (CHAIN A) AND PROXIMAL UBIQUITIN (CHAIN B) ARE CONNECTED VIA A COVALENT LINKAGE BETWEEN C GLY 76 OF CHAIN A AND NZ LYS 11 OF CHAIN B. THIS LINKAGE HAS NOT BEEN MODELED IN THIS STRUCTURE.

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-15N IPAP HSQC

Sample preparation

• Details: Contents: 75 uM [U-99% 15N] ubiquitin, 20 mM sodium phosphate, 150 mM sodium chloride, 93% H2O/7% D2O; Solvent system: 93% H2O/7% D2O

Sample

Conc. (mg/ml)	Component	Isotopic labeling	Solution-ID
75 uM	entity-1	[U-99% 15N]	1
20 mM	sodium phosphate-2		1
150 mM	sodium chloride-3		1

• Sample conditions: Ionic strength: 150 / pH: 6.8 / Pressure: ambient / Temperature: 296 K

NMR measurement

• NMR spectrometer: Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

Processing

NMR software

Name	Version	Developer	Classification
TopSpin	2.1	Bruker Biospin	collection
NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax	processing
Sparky		Goddard	chemical shift assignment
in-house			refinement

• Refinement: Method: in-house RDC (orientation), MTSL (distance) / Software ordinal: 1 ; Details: Ub/Ub orientation determined from RDCs via alignment tensors, and Z-distance refined using site-directed spin labeling distance constraints (MTSL on distal position 36) from 0 mM NaCl structure. No MTSL data was collected at 150 mM NaCl.
• NMR representative: Selection criteria: closest to the average
• NMR ensemble: Conformer selection criteria: target function / Conformers calculated total number: 1 / Conformers submitted total number: 1