- PDB-2kdf: NMR structure of minor S5a (196-306):K48 linked diubiquitin species -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2kdf
Title
NMR structure of minor S5a (196-306):K48 linked diubiquitin species
Components
26S proteasome non-ATPase regulatory subunit 4
Ubiquitin
Keywords
PROTEIN BINDING / protein complex / ubiquitin interacting motifs / Cytoplasm / Nucleus / Phosphoprotein / Ubl conjugation / Alternative splicing / Proteasome
Function / homology
Function and homology information
: / : / protein modification process => GO:0036211 / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / Peptide chain elongation / Selenocysteine synthesis ...: / : / protein modification process => GO:0036211 / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / 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 / polyubiquitin modification-dependent protein binding / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / 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 / proteasome complex / 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 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / 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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway Similarity search - Function
: / Ubiquitin interaction motif / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Ribosomal L40e family / Ribosomal_L40e ...: / Ubiquitin interaction motif / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / von Willebrand factor, type A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / von Willebrand factor A-like domain superfamily / 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
Mass: 11826.878 Da / Num. of mol.: 1 / Fragment: UNP residues 196-306, S5a fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4, MCB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55036
#2: Protein
Ubiquitin
Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 1H-15N NOESY
2
2
2
3D 1H-13C NOESY
2
3
3
3D 13C-filtered 1H-13C NOESY
2
4
4
3D 13C-filtered 1H-13C NOESY
2
5
5
3D 13C-filtered 1H-13C NOESY
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.4 mM [U-100% 15N; U-50% 2H] S5a (196-306)-1, 1.2 mM K48 linked diubiquitin-2, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.5 mM [U-100% 13C] S5a (196-306)-3, 1.5 mM K48 linked diubiquitin-4, 100% D2O
100% D2O
3
0.5 mM [U-100% 13C of the proximal Ub; natural abundance of the distal subunit] K48 linked diubiquitin-5, 1.0 mM S5a (196-306)-6, 100% D2O
100% D2O
4
0.5 mM [U-100% 13C of the distal subunit; natural abundance of the proximal Ub] K48 linked diubiquitin-7, 1.0 mM S5a (196-306)-8, 100% D2O
100% D2O
5
0.4 mM [U-100% 13C] S5a (196-306)-9, 1.2 mM [U-100% 2H of the proximal Ub; natural abundance of the distal subunit] K48 linked diubiquitin-10, 100% D2O
100% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.4mM
S5a (196-306)-1
[U-100% 15N; U-50% 2H]
1
1.2mM
K48 linked diubiquitin-2
1
0.5mM
S5a (196-306)-3
[U-100% 13C]
2
1.5mM
K48 linked diubiquitin-4
2
0.5mM
K48 linked diubiquitin-5
[U-100% 13C of the proximal Ub; natural abundance of the distal subunit]
3
1.0mM
S5a (196-306)-6
3
0.5mM
K48 linked diubiquitin-7
[U-100% 13C of the distal subunit; natural abundance of the proximal Ub]
4
1.0mM
S5a (196-306)-8
4
0.4mM
S5a (196-306)-9
[U-100% 13C]
5
1.2mM
K48 linked diubiquitin-10
[U-100% 2H of the proximal Ub; natural abundance of the distal subunit]
5
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
20mMNaPO4; 100mMNaCl
6.5
ambient
298K
2
20mMNaPO4; 50mMNaCl
6.5
ambient
298K
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
800
1
Varian INOVA
Varian
INOVA
900
2
-
Processing
NMR software
Name
Developer
Classification
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
XEASY
Bartelsetal.
dataanalysis
X-PLOR
Brunger
structuresolution
X-PLOR
Brunger
refinement
Refinement
Method: simulated annealing / Software ordinal: 1
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 7
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi