[English] 日本語
Yorodumi
- PDB-5nli: Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EHV

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 %

+
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.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more