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- PDB-5tog: Room temperature structure of ubiquitin variant u7ub25.2540 -

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Basic information

Entry
Database: PDB / ID: 5tog
TitleRoom temperature structure of ubiquitin variant u7ub25.2540
ComponentsPolyubiquitin-B
KeywordsSIGNALING PROTEIN / COMPUTATIONALLY DESIGNED UBIQUITIN / USP7
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neuron apoptotic process ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / 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 / 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) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / neuron projection morphogenesis / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Stabilization of p53
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsBiel, J.T. / Thompson, M.C. / Cunningham, C.N. / Corn, J.E. / Fraser, J.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5 OD009180 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21 GM110580 United States
National Science Foundation (NSF, United States)STC-1231306 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F32 HL129989 United States
CitationJournal: Structure / Year: 2017
Title: Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin.
Authors: Biel, J.T. / Thompson, M.C. / Cunningham, C.N. / Corn, J.E. / Fraser, J.S.
History
DepositionOct 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1023
Polymers8,9101
Non-polymers1922
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Polyubiquitin-B
hetero molecules

A: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2056
Polymers17,8202
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1720 Å2
ΔGint-55 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.920, 43.920, 55.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-102-

SO4

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Components

#1: Protein Polyubiquitin-B / U7Ub25.2540


Mass: 8910.185 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.79 Å3/Da / Density % sol: 31.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1ul protein solution at 10 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.2, 2.2 M ammonium sulfate)

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.08→38.04 Å / Num. obs: 27011 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 8.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 28.21
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.08-1.110.4914.220.909196.8
1.11-1.140.3626.560.964199.9
1.14-1.170.2938.220.9761100
1.17-1.210.23610.270.9851100
1.21-1.250.20811.920.9881100
1.25-1.290.17913.990.9911100
1.29-1.340.16515.060.9931100
1.34-1.390.12819.680.9951100
1.39-1.460.10923.070.9961100
1.46-1.530.08628.350.9981100
1.53-1.610.0733.330.9981100
1.61-1.710.0638.840.9991100
1.71-1.830.04946.560.9991100
1.83-1.970.0452.740.9991100
1.97-2.160.03659.960.9991100
2.16-2.420.03364.360.9991100
2.42-2.790.0368.611199.8
2.79-3.420.02773.9611100
3.42-4.830.02674.380.999199.2
4.83-38.040.02671.290.999195.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.11_2556refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UQB

1uqb


Resolution: 1.08→38.036 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 9.43
RfactorNum. reflection% reflection
Rfree0.1211 1574 5.83 %
Rwork0.1032 --
obs0.1042 27008 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 47.74 Å2 / Biso mean: 11.3588 Å2 / Biso min: 4.57 Å2
Refinement stepCycle: final / Resolution: 1.08→38.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms607 0 10 101 718
Biso mean--17.13 23.4 -
Num. residues----75
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091267
X-RAY DIFFRACTIONf_angle_d1.0491691
X-RAY DIFFRACTIONf_chiral_restr0.081188
X-RAY DIFFRACTIONf_plane_restr0.008211
X-RAY DIFFRACTIONf_dihedral_angle_d14.008490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.08-1.11490.16181370.12072231236897
1.1149-1.15480.13931400.090223092449100
1.1548-1.2010.10391410.078622792420100
1.201-1.25570.10811450.077122892434100
1.2557-1.32190.10721440.075622742418100
1.3219-1.40470.1121410.074422962437100
1.4047-1.51310.10691460.076323252471100
1.5131-1.66540.10481370.080922982435100
1.6654-1.90640.10781460.089923472493100
1.9064-2.40180.11411440.103723482492100
2.4018-38.05940.13841530.13312438259199

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