[English] 日本語
Yorodumi
- PDB-3ehv: X-ray structure of human ubiquitin Zn(II) adduct -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ehv
TitleX-ray structure of human ubiquitin Zn(II) adduct
ComponentsUbiquitin
KeywordsLIGASE / human ubiquitin / adduct
Function / homology
Function and homology information


Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol ...Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / L13a-mediated translational silencing of Ceruloplasmin expression / protein modification process => GO:0036211 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / extrinsic component of mitochondrial outer membrane / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / CDT1 association with the CDC6:ORC:origin complex / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / Constitutive Signaling by NOTCH1 HD Domain Mutants / Negative regulation of FLT3 / TICAM1-dependent activation of IRF3/IRF7 / 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 / Regulation of BACH1 activity / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of innate immune responses to cytosolic DNA / TRAF6-mediated induction of TAK1 complex within TLR4 complex / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / Pexophagy / InlA-mediated entry of Listeria monocytogenes into host cells / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of ERBB2:ERBB3 signaling / 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) / Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / InlB-mediated entry of Listeria monocytogenes into host cell / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / 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 / Recognition of DNA damage by PCNA-containing replication complex / ROS sensing by NFE2L2 / 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 / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vif-mediated degradation of APOBEC3G / Negative regulators of DDX58/IFIH1 signaling / Degradation of GLI1 by the proteasome / DNA Damage Recognition in GG-NER / 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 / Hedgehog 'on' state / activated TAK1 mediates p38 MAPK activation
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e superfamily / Ribosomal protein L40e / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e superfamily / Ribosomal protein L40e / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like (UB roll) / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsFalini, G. / Fermani, S. / Tosi, G.
CitationJournal: Chem.Commun.(Camb.) / Year: 2008
Title: Structural probing of Zn(II), Cd(II) and Hg(II) binding to human ubiquitin.
Authors: Falini, G. / Fermani, S. / Tosi, G. / Arnesano, F. / Natile, G.
History
DepositionSep 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7964
Polymers25,7303
Non-polymers651
Water2,288127
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6422
Polymers8,5771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,5771
Polymers8,5771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,5771
Polymers8,5771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.357, 50.946, 93.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 3
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, ubiquitin-protein ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 25mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 26, 2007
RadiationMonochromator: double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→32.5 Å / Num. all: 19140 / Num. obs: 19094 / % possible obs: 94.8 % / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.0101 / Rsym value: 0.114 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 1.3 / Num. unique all: 302 / Rsym value: 0.513 / % possible all: 30.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 1.81→32.15 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3191116.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): 5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 931 4.9 %RANDOM
Rwork0.222 ---
obs0.222 19094 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.0679 Å2 / ksol: 0.353035 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å20 Å20 Å2
2--0.96 Å20 Å2
3---1.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-8 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.81→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 1 127 1831
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.642
X-RAY DIFFRACTIONc_scangle_it4.112.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 115 4.9 %
Rwork0.298 2249 -
obs-302 71.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.param

+
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