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- PDB-3v6e: Crystal Structure of USP2 and a mutant form of Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 3v6e
TitleCrystal Structure of USP2 and a mutant form of Ubiquitin
Components
  • Ubiquitin
  • Ubiquitin carboxyl-terminal hydrolase 2
Keywordshydrolase/signaling protein / Structural Genomics / Structural Genomics Consortium / SGC / ubiquitin / protease / hydrolase-signaling protein complex
Function / homology
Function and homology information


circadian behavior / TNFR1-induced proapoptotic signaling / muscle organ development / entrainment of circadian clock by photoperiod / locomotor rhythm / protein deubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora ...circadian behavior / TNFR1-induced proapoptotic signaling / muscle organ development / entrainment of circadian clock by photoperiod / locomotor rhythm / protein deubiquitination / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / positive regulation of mitotic cell cycle / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / cyclin binding / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / 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 REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / regulation of signal transduction by p53 class mediator / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Regulation of TNFR1 signaling / circadian regulation of gene expression / Hh mutants are degraded by ERAD
Similarity search - Function
: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A ...: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 2 / Polyubiquitin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsNeculai, M. / Ernst, A. / Sidhu, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Science / Year: 2013
Title: A strategy for modulation of enzymes in the ubiquitin system.
Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / ...Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / Juang, Y.C. / Landry, M.C. / Yeh, C. / Zeqiraj, E. / Karamboulas, K. / Allali-Hassani, A. / Vedadi, M. / Tyers, M. / Moffat, J. / Sicheri, F. / Pelletier, L. / Durocher, D. / Raught, B. / Rotin, D. / Yang, J. / Moran, M.F. / Dhe-Paganon, S. / Sidhu, S.S.
History
DepositionDec 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7446
Polymers52,5152
Non-polymers2284
Water3,549197
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-29 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.097, 84.124, 87.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ubiquitin carboxyl-terminal hydrolase 2 / 41 kDa ubiquitin-specific protease / Deubiquitinating enzyme 2 / Ubiquitin thiolesterase 2 / ...41 kDa ubiquitin-specific protease / Deubiquitinating enzyme 2 / Ubiquitin thiolesterase 2 / Ubiquitin-specific-processing protease 2


Mass: 42171.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBP41, usp02.258.605, USP2 / Plasmid: PET28LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75604, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin


Mass: 10343.754 Da / Num. of mol.: 1 / Mutation: G76S, K82N, T85S, T88H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: PET53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG48

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Non-polymers , 4 types, 201 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 21% PEG3350, 0.2 M Calcium Chloride,0.1 Bis-Tris pH 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→85 Å / Num. all: 29672 / Num. obs: 29660 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.04 % / Rsym value: 0.1589 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.04 Å / Redundancy: 6.98 % / Mean I/σ(I) obs: 3.01 / Num. unique all: 1252 / Rsym value: 0.5588 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2HD5

2hd5


Resolution: 2.1→42.06 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.2018 / WRfactor Rwork: 0.15 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8767 / SU B: 4.375 / SU ML: 0.119 / SU R Cruickshank DPI: 0.2261 / SU Rfree: 0.1937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1283 5 %RANDOM
Rwork0.1735 ---
all0.1766 25647 --
obs0.1766 25647 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.81 Å2 / Biso mean: 15.1054 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 9 197 3482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213536
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9564801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7555447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16223.222180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60115634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2571535
X-RAY DIFFRACTIONr_chiral_restr0.0890.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212729
X-RAY DIFFRACTIONr_mcbond_it0.7061.52128
X-RAY DIFFRACTIONr_mcangle_it1.31823463
X-RAY DIFFRACTIONr_scbond_it1.80931408
X-RAY DIFFRACTIONr_scangle_it2.9154.51325
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 93 -
Rwork0.192 1769 -
all-1862 -
obs--100 %

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