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- PDB-2pe9: NMR Based Structure of the Open Conformation of LYS48-Linked Di-U... -

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Basic information

Entry
Database: PDB / ID: 2pe9
TitleNMR Based Structure of the Open Conformation of LYS48-Linked Di-UBiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN / UBIQUITIN / LYS48-LINKED POLYUBIQUITIN / POLYUBIQUITIN
Function / homology
Function and homology information


: / : / protein modification process => GO:0036211 / 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 / Viral mRNA Translation ...: / : / protein modification process => GO:0036211 / 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 / 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) / 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 / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / cytosolic ribosome / 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 / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / 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 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / 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 REV1 / 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 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsRyabov, Y. / Fushman, D.
Citation
Journal: J.Am.Chem.Soc. / Year: 2007
Title: Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.
Authors: Ryabov, Y. / Fushman, D.
#1: Journal: J.Am.Chem.Soc. / Year: 2006
Title: An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation.
Authors: Ryabov, Y. / Geraghty, C. / Varshney, A. / Fushman, D.
#2: Journal: J.Am.Chem.Soc. / Year: 2007
Title: A Model of Interdomain Mobility in a Multidomain Protein
Authors: Ryabov, Y. / Fushman, D.
#3: Journal: J.Mol.Biol. / Year: 2002
Title: Structural Properties of Polyubiquitin Chains in Solution
Authors: Varadan, R. / Walker, O. / Picart, C. / Fushman, D.
History
DepositionApr 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1542
Polymers17,1542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -structures with the lowest energy
Representativelowest energy

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Components

#1: Protein Ubiquitin / UBIQUITIN


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N T1
12115N T2
131HETERONUCLEAR NOE
141HSQC
151TOCSY

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Sample preparation

DetailsContents: DI-UBIQUITIN, 90% WATER/10% D20
Sample conditionsIonic strength: 20mM / pH: 6.8 / Pressure: AMBIENT / Temperature: 298.0 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ELMstructure solution
ELMY.RYABOV, D.FUSHMANrefinement
RefinementSoftware ordinal: 1
Details: THE STRUCTURE WAS DETERMINED WITH PROGRAM ELM USING COMPLETE ROTATIONAL DIFFUSION TENSOR OF DI- UBIQUITIN AS EXPERIMENTAL RESTRAINT FOR BOTH ORIENTATION AND POSITIONING OF THE INDIVIDUAL ...Details: THE STRUCTURE WAS DETERMINED WITH PROGRAM ELM USING COMPLETE ROTATIONAL DIFFUSION TENSOR OF DI- UBIQUITIN AS EXPERIMENTAL RESTRAINT FOR BOTH ORIENTATION AND POSITIONING OF THE INDIVIDUAL UBIQUITIN DOMAINS WITHIN THE MOLECULE. UBIQUITIN DOMAINS WHERE ORIENTED BY A RIGID BODY ROTATION USING EXPERIMENTALLY DERIVED PRINCIPAL AXES FRAME OF THE DIFFUSION TENSOR (SEE REFERENCE 2). THE RELATIVE DOMAIN POSITIONS IN DI-UBIQUITIN WERE DETERMINED BY A RIGID BODY TRANSLATION USING ALL COMPONENTS OF THE EXPERIMENTALLY DERIVED ROTATIONAL DIFFUSION TENSOR AS RESTRAINTS. FOR EACH UBIQUITIN DOMAIN THE STRUCTURE OF THE FIRST CONFORMER OF PDB ENTRY 1D3Z WAS ASSUMED. THE DEPOSITED CONFORMATION REPRESENTS ONE OF THE TWO EXPERIMENTALLY DETECTABLE CONFORMATIONS OF DI-UBIQUITIN AT PH 6.8. THE OCCUPATION PROBABILITY OF THIS CONFORMATION IS APPROXIMATELY 10%. CHAIN A CORRESPONDS TO UBIQUITIN DOMAIN THAT HAS A FREE C-TERMINUS IN DI-UBIQUITIN. CHAIN B CORRESPONDS TO UBIQUITIN DOMAIN THAT IN DI-UBIQUITIN IS LINKED VIA AN ISOPEPTIDE BOND BETWEEN ITS C- TERMINAL GLY76 AND LYS48 OF CHAIN A. THE ISOPEPTIDE BOND WAS PRESENT IN THE DI-UBIQUITIN MOLECULE IN THIS STUDY. HOWEVER, BECAUSE THIS STRUCTURE WAS OBTAINED BY A RIGID BODY ROTATION AND TRANSLATION AND NO CONSTRAINTS REPRESENTING THE INTERDOMAIN LINKAGE WERE INCLUDED, THE ISOPEPTIDE LINKAGE IS NOT PRESENT IN THE STRUCTURE. FLEXIBLE C-TERMINI OF BOTH UBIQUTIN DOMAINS (RESIDUES 73-76)WERE EXCLUDED FROM THE NMR DATA ANALYSIS AND THEREFORE ARE NOT PRESENT IN THIS STRUCTURE.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers submitted total number: 1

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