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- PDB-3ehv: X-ray structure of human ubiquitin Zn(II) adduct -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 2.05 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

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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

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Processing

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

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