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- PDB-2mur: Solution Structure of the Human FAAP20 UBZ-Ubiquitin Complex -

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Basic information

Entry
Database: PDB / ID: 2mur
TitleSolution Structure of the Human FAAP20 UBZ-Ubiquitin Complex
Components
  • Fanconi anemia-associated protein of 20 kDa
  • Ubiquitin
KeywordsPROTEIN BINDING / UBZ / FAAP20 / zinc-finger / Fanconi Anemia
Function / homology
Function and homology information


Fanconi anaemia nuclear complex / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / 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 / polyubiquitin modification-dependent protein binding ...Fanconi anaemia nuclear complex / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / 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 / polyubiquitin modification-dependent protein binding / 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 / translesion synthesis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / interstrand cross-link repair / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / cytosolic ribosome / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / 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 / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway
Similarity search - Function
FAAP20, zinc finger UBZ2-type / FAAP20, FANCA interaction domain / : / Ubiquitin-binding zinc-finger / FAAP20 FANCA interaction domain / Zinc finger UBZ2-type profile. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily ...FAAP20, zinc finger UBZ2-type / FAAP20, FANCA interaction domain / : / Ubiquitin-binding zinc-finger / FAAP20 FANCA interaction domain / Zinc finger UBZ2-type 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
Ubiquitin-ribosomal protein eL40 fusion protein / Fanconi anemia core complex-associated protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsWang, S. / Wojtaszek, J.L. / Zhou, P.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Ubiquitin recognition by FAAP20 expands the complex interface beyond the canonical UBZ domain.
Authors: Wojtaszek, J.L. / Wang, S. / Kim, H. / Wu, Q. / D'Andrea, A.D. / Zhou, P.
History
DepositionSep 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fanconi anemia-associated protein of 20 kDa
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7213
Polymers13,6562
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Fanconi anemia-associated protein of 20 kDa


Mass: 4853.492 Da / Num. of mol.: 1 / Fragment: UBZ, UNP residues 140-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1orf86, FAAP20, FP7162 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NZ36
#2: Protein Ubiquitin


Mass: 8802.056 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA52, UBCEP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62987
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1364D sparse-sampled (H)CCH TOCSY
1413D sparse-sampled HA(CA)NH
1513D sparse-sampled HNCO
1613D sparse-sampled HNCA
1713D sparse-sampled HN(CA)CB
1813D sparse-sampled HN(CO)CA
1913D sparse-sampled HN(COCA)CB
11014D sparse-sampled HC(CO)NH-TOCSY
11114D sparse-sampled CHNH NOESY
11213D 1H-15N NOESY
11323D sparse-sampled HA(CACO)NH
11423D sparse-sampled HA(CA)NH
11523D sparse-sampled HNCO
11623D sparse-sampled HNCA
11723D sparse-sampled HN(CA)CB
11823D sparse-sampled HN(CO)CA
11924D sparse-sampled HC(CO)NH-TOCSY
12024D sparse-sampled CHNH NOESY
12123D sparse-sampled HN(COCA)CB
12223D 1H-15N NOESY
12334D sparse-sampled CHCH NOESY
12444D sparse-sampled CHCH NOESY
12554D sparse-sampled CHCH NOESY
12623D sparse-sampled HN(CA)CO
12774D sparse-sampled (H)CCH TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 2 mM UBZ, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] UBZ, 0.8 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
33 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 3 mM [U-100% 13C; U-100% 15N] UBZ, 100% D2O100% D2O
43 mM Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 3 mM [U-100% 13C; U-100% 15N] UBZ, 100% D2O100% D2O
53 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 3 mM UBZ, 100% D2O100% D2O
61 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 2 mM UBZ, 100% D2O100% D2O
70.8 mM [U-100% 13C; U-100% 15N] UBZ, 0.8 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMUbiquitin-1[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate-21
100 mMpotassium chloride-31
2 mMUBZ-41
0.8 mMUBZ-5[U-100% 13C; U-100% 15N]2
0.8 mMUbiquitin-6[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-72
100 mMpotassium chloride-82
3 mMUbiquitin-9[U-100% 13C; U-100% 15N]3
25 mMsodium phosphate-103
100 mMpotassium chloride-113
3 mMUBZ-12[U-100% 13C; U-100% 15N]3
3 mMUbiquitin-134
25 mMsodium phosphate-144
100 mMpotassium chloride-154
3 mMUBZ-16[U-100% 13C; U-100% 15N]4
3 mMUbiquitin-17[U-100% 13C; U-100% 15N]5
25 mMsodium phosphate-185
100 mMpotassium chloride-195
3 mMUBZ-205
1 mMUbiquitin-21[U-100% 13C; U-100% 15N]6
25 mMsodium phosphate-226
100 mMpotassium chloride-236
2 mMUBZ-246
0.8 mMUBZ-25[U-100% 13C; U-100% 15N]7
0.8 mMUbiquitin-26[U-100% 13C; U-100% 15N]7
25 mMsodium phosphate-277
100 mMpotassium chloride-287
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
SCRUBCoggins and Zhouprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
XEASYBartels et al.data analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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