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- PDB-3wxe: Crystal structure of CYLD USP domain (C596S) in complex with Met1... -

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Basic information

Entry
Database: PDB / ID: 3wxe
TitleCrystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin
Components
  • Ubiquitin
  • Uncharacterized protein
KeywordsHYDROLASE/PROTEIN BINDING / ubiquitin protease / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / Ub-specific processing proteases / protein linear deubiquitination / regulation of intrinsic apoptotic signaling pathway / central nervous system morphogenesis / negative regulation of p38MAPK cascade / cranial skeletal system development / negative regulation of JNK cascade / positive regulation of extrinsic apoptotic signaling pathway ...Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / Ub-specific processing proteases / protein linear deubiquitination / regulation of intrinsic apoptotic signaling pathway / central nervous system morphogenesis / negative regulation of p38MAPK cascade / cranial skeletal system development / negative regulation of JNK cascade / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of non-canonical NF-kappaB signal transduction / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / necroptotic process / regulation of embryonic development / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / regulation of mitotic cell cycle / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / 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 / cell projection / 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 / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN
Similarity search - Function
Phosphorylation region of CYLD, unstructured / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase ...Phosphorylation region of CYLD, unstructured / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / 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 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase CYLD / Polyubiquitin-C
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSato, Y. / Fukai, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.
Authors: Sato, Y. / Goto, E. / Shibata, Y. / Kubota, Y. / Yamagata, A. / Goto-Ito, S. / Kubota, K. / Inoue, J. / Takekawa, M. / Tokunaga, F. / Fukai, S.
History
DepositionJul 30, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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: Uncharacterized protein
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)52,7432
Polymers52,7432
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-9 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.676, 49.788, 71.003
Angle α, β, γ (deg.)90.00, 102.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein / CYLD protein


Mass: 35991.520 Da / Num. of mol.: 1 / Fragment: USP domain, UNP residues 578-780, Linker, 850-951 / Mutation: C596S, B-box deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cyld, cylda / Plasmid: pColdI / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: E7FEV5
#2: Protein Ubiquitin / M1-linked diubiquitin


Mass: 16751.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50mM Tris-HCl buffer, 9% PEG4000, 100mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 20, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 15549 / Num. obs: 15549 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Rsym value: 0.094
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.329 / % possible all: 92.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VHF and 1UBQ

2vhf

1ubq


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 25.355 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24722 766 5.1 %RANDOM
Rwork0.18191 ---
obs0.18518 14287 96.97 %-
all-15549 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.063 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å2-0 Å20.45 Å2
2---1.2 Å2-0 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 0 47 3664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193684
X-RAY DIFFRACTIONr_bond_other_d0.0020.023587
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9824965
X-RAY DIFFRACTIONr_angle_other_deg0.85538286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2724.647170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82815702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1561521
X-RAY DIFFRACTIONr_chiral_restr0.0810.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3063.3661793
X-RAY DIFFRACTIONr_mcbond_other3.3053.3631792
X-RAY DIFFRACTIONr_mcangle_it5.3645.0372236
X-RAY DIFFRACTIONr_mcangle_other5.3635.0392237
X-RAY DIFFRACTIONr_scbond_it4.2643.7861891
X-RAY DIFFRACTIONr_scbond_other4.2633.7871891
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4395.5012729
X-RAY DIFFRACTIONr_long_range_B_refined9.02126.3814014
X-RAY DIFFRACTIONr_long_range_B_other9.01526.3834006
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 70 -
Rwork0.29 962 -
obs--91.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1198-0.212-0.09061.5197-0.12520.51120.0280.073-0.04670.262-0.13470.1927-0.01810.03110.10670.1613-0.02630.06090.1241-0.02880.06215.43872.235619.607
23.2501-0.7429-1.68491.01590.22070.95320.2119-0.0708-0.2677-0.2757-0.25180.2639-0.11480.04950.03980.1220.0941-0.0190.1367-0.01650.13227.7501-3.05182.1088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A577 - 885
2X-RAY DIFFRACTION2B1 - 148

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