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- PDB-4i6n: Crystal structure of Trichinella spiralis UCH37 catalytic domain ... -

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Basic information

Entry
Database: PDB / ID: 4i6n
TitleCrystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl methyl ester
Components
  • Ubiquitin
  • Ubiquitin carboxyl-hydrolase
KeywordsHydrolase/Signaling Protein / helix-beta-helix sandwich / protein-protein complex / deubiquitination / ubiquitin c-terminal hydrolase / cytosol / Hydrolase-Signaling Protein complex
Function / homology
Function and homology information


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 ...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 / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR2 signaling / Degradation of DVL / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis / Degradation of AXIN / Hh mutants are degraded by ERAD / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Activation of NF-kappaB in B cells / Iron uptake and transport / Recognition of DNA damage by PCNA-containing replication complex / Assembly Of The HIV Virion / Degradation of GLI1 by the proteasome / Spry regulation of FGF signaling / Hedgehog ligand biogenesis
Similarity search - Function
Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / METHYL 4-AMINOBUTANOATE / Polyubiquitin-C
Similarity search - Component
Biological speciesTrichinella spiralis (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.701 Å
AuthorsMorrow, M.E. / Ronau, J.A. / White, R.R. / Artavanis-Tsakonas, K. / Das, C.
CitationJournal: Biochemistry / Year: 2013
Title: Stabilization of an Unusual Salt Bridge in Ubiquitin by the Extra C-Terminal Domain of the Proteasome-Associated Deubiquitinase UCH37 as a Mechanism of Its Exo Specificity.
Authors: Morrow, M.E. / Kim, M.I. / Ronau, J.A. / Sheedlo, M.J. / White, R.R. / Chaney, J. / Paul, L.N. / Lill, M.A. / Artavanis-Tsakonas, K. / Das, C.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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-hydrolase
B: Ubiquitin
C: Ubiquitin carboxyl-hydrolase
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0758
Polymers69,6634
Non-polymers4124
Water6,233346
1
A: Ubiquitin carboxyl-hydrolase
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1265
Polymers34,8322
Non-polymers2943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-27 kcal/mol
Surface area13520 Å2
MethodPISA
2
C: Ubiquitin carboxyl-hydrolase
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9493
Polymers34,8322
Non-polymers1171
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-14 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.202, 55.759, 73.868
Angle α, β, γ (deg.)90.00, 113.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-215-

HOH

21B-218-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Ubiquitin carboxyl-hydrolase


Mass: 26265.002 Da / Num. of mol.: 2 / Fragment: catalytic domain residues 1-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichinella spiralis (invertebrata) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
#2: Protein Ubiquitin


Mass: 8566.673 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P0CG48

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Non-polymers , 4 types, 350 molecules

#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GVE / METHYL 4-AMINOBUTANOATE


Type: peptide-like / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 3M ammonium sulfate, 0.1M bicine, 2mM L-glutathione, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 6, 2012
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 62326 / Num. obs: 62326 / % possible obs: 88.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 20.04 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.73 Å / % possible all: 42

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Processing

Software
NameVersionClassification
HKL-3000data collection
AutoSol(PHENIX.AUTOSOL)phasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.701→27.88 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 3133 5.03 %random
Rwork0.1744 ---
obs0.1763 62257 88.35 %-
all-70466 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.701→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 25 346 4990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174767
X-RAY DIFFRACTIONf_angle_d1.7536451
X-RAY DIFFRACTIONf_dihedral_angle_d15.6471787
X-RAY DIFFRACTIONf_chiral_restr0.122736
X-RAY DIFFRACTIONf_plane_restr0.008830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7006-1.72720.293590.2761235X-RAY DIFFRACTION41
1.7272-1.75550.3321750.24561431X-RAY DIFFRACTION47
1.7555-1.78580.2836660.23691666X-RAY DIFFRACTION54
1.7858-1.81830.2436870.24271839X-RAY DIFFRACTION61
1.8183-1.85320.30211280.23632193X-RAY DIFFRACTION72
1.8532-1.8910.30341120.2422474X-RAY DIFFRACTION82
1.891-1.93210.25391570.2342771X-RAY DIFFRACTION92
1.9321-1.97710.26521620.20912857X-RAY DIFFRACTION96
1.9771-2.02650.23551780.19482990X-RAY DIFFRACTION99
2.0265-2.08130.2421630.18452976X-RAY DIFFRACTION99
2.0813-2.14250.24181510.18613088X-RAY DIFFRACTION100
2.1425-2.21160.22461770.17812992X-RAY DIFFRACTION100
2.2116-2.29060.2351480.17623035X-RAY DIFFRACTION100
2.2906-2.38230.24021580.18183057X-RAY DIFFRACTION100
2.3823-2.49070.24171720.18163019X-RAY DIFFRACTION100
2.4907-2.62190.24451670.19033028X-RAY DIFFRACTION100
2.6219-2.7860.24631690.19343056X-RAY DIFFRACTION100
2.786-3.00090.20991700.193009X-RAY DIFFRACTION100
3.0009-3.30250.21551460.17633087X-RAY DIFFRACTION100
3.3025-3.77930.17851500.14443070X-RAY DIFFRACTION100
3.7793-4.75770.15861710.12773080X-RAY DIFFRACTION100
4.7577-27.88320.16671670.16333171X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 35.4692 Å / Origin y: 51.0532 Å / Origin z: 17.3875 Å
111213212223313233
T0.2773 Å20.0143 Å20.0083 Å2-0.2452 Å20.008 Å2--0.264 Å2
L0.7776 °2-0.2111 °21.1152 °2-0.0699 °2-0.4289 °2--1.7801 °2
S0.0156 Å °0.1582 Å °0.0021 Å °-0.023 Å °-0.0525 Å °-0.0208 Å °-0.0073 Å °0.233 Å °0.0413 Å °
Refinement TLS groupSelection details: all

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