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- PDB-5nli: Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct... -

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Basic information

Entry
Database: PDB / ID: 5nli
TitleCrystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/10% v/v TFE/1.3 mM E16V hUb
ComponentsPolyubiquitin-C
KeywordsLIGASE / E16V mutant / ubiquitination / proteasome degradation
Function / homology
Function and homology information


extrinsic component of mitochondrial outer membrane / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / Glycogen synthesis / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway ...extrinsic component of mitochondrial outer membrane / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / Glycogen synthesis / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Regulation of FZD by ubiquitination / IRAK1 recruits IKK complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Constitutive Signaling by NOTCH1 HD Domain Mutants / Negative regulation of FLT3 / Membrane binding and targetting of GAG proteins / TICAM1-dependent activation of IRF3/IRF7 / 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 / Regulation of BACH1 activity / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / APC-Cdc20 mediated degradation of Nek2A / Pexophagy / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / NRIF signals cell death from the nucleus / Translesion synthesis by REV1 / Regulation of PTEN localization / NF-kB is activated and signals survival / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Gap-filling DNA repair synthesis and ligation in GG-NER / Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon / Translesion synthesis by POLI / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / Downregulation of TGF-beta receptor signaling / IKK complex recruitment mediated by RIP1 / CDT1 association with the CDC6:ORC:origin complex / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Recognition of DNA damage by PCNA-containing replication complex / Autodegradation of Cdh1 by Cdh1:APC/C / Degradation of DVL / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / TNFR1-induced NFkappaB signaling pathway / Ubiquitin-dependent degradation of Cyclin D / Regulation of TNFR1 signaling / TCF dependent signaling in response to WNT / Vpu mediated degradation of CD4 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / Vif-mediated degradation of APOBEC3G / DNA Damage Recognition in GG-NER / Negative regulators of DDX58/IFIH1 signaling / Degradation of GLI1 by the proteasome / Dectin-1 mediated noncanonical NF-kB signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Hh mutants are degraded by ERAD / Negative regulation of NOTCH4 signaling / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Regulation of signaling by CBL / activated TAK1 mediates p38 MAPK activation / Hedgehog 'on' state / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Activation of NF-kappaB in B cells / Peroxisomal protein import / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Iron uptake and transport / Degradation of AXIN / GLI3 is processed to GLI3R by the proteasome / Degradation of GLI2 by the proteasome / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / G2/M Checkpoints / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex
Similarity search - Function
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
ACETATE ION / TRIFLUOROETHANOL / Polyubiquitin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsFermani, S. / Falini, G.
Citation
Journal: Chemistry / Year: 2018
Title: Aggregation Pathways of Native-Like Ubiquitin Promoted by Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium.
Authors: Fermani, S. / Calvaresi, M. / Mangini, V. / Falini, G. / Bottoni, A. / Natile, G. / Arnesano, F.
#1: Journal: Chemistry / Year: 2013
Title: Conformational selection of ubiquitin quaternary structures driven by zinc ions.
Authors: Fermani, S. / Falini, G. / Calvaresi, M. / Bottoni, A. / Calo, V. / Mangini, V. / Arnesano, F. / Natile, G.
History
DepositionApr 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-C
B: Polyubiquitin-C
C: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,55217
Polymers25,6413
Non-polymers91214
Water4,216234
1
A: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,11010
Polymers8,5471
Non-polymers5639
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8365
Polymers8,5471
Non-polymers2904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6062
Polymers8,5471
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.450, 50.730, 93.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Polyubiquitin-C


Mass: 8546.848 Da / Num. of mol.: 3 / Mutation: E16V
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

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Non-polymers , 5 types, 248 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3F3O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22-30% (w/v) PEG 1450, 50 mM HEPES, 35 mM Zn(CH3COO)2 and 10% v/v TFE
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.265 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 16, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.265 Å / Relative weight: 1
ReflectionResolution: 1.53→27.22 Å / Num. obs: 31309 / % possible obs: 95.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rsym value: 0.085 / Net I/σ(I): 15
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3417 / Rsym value: 0.293 / % possible all: 73.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EHV
Resolution: 1.53→26.61 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.202 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20154 1536 4.9 %RANDOM
Rwork0.16716 ---
obs0.16893 29709 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.813 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0 Å2-0 Å2
2--0.82 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.53→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 40 234 2029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191844
X-RAY DIFFRACTIONr_bond_other_d0.0020.021903
X-RAY DIFFRACTIONr_angle_refined_deg2.2582.0062486
X-RAY DIFFRACTIONr_angle_other_deg1.09434392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89325.30981
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27915377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7421513
X-RAY DIFFRACTIONr_chiral_restr0.1470.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02373
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7891.486896
X-RAY DIFFRACTIONr_mcbond_other1.7581.478890
X-RAY DIFFRACTIONr_mcangle_it2.6332.2031112
X-RAY DIFFRACTIONr_mcangle_other2.6332.2071113
X-RAY DIFFRACTIONr_scbond_it3.2291.966948
X-RAY DIFFRACTIONr_scbond_other3.2211.965948
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9132.7831368
X-RAY DIFFRACTIONr_long_range_B_refined7.24213.562134
X-RAY DIFFRACTIONr_long_range_B_other7.24313.5462134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 71 -
Rwork0.203 1480 -
obs--65.36 %

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