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- PDB-3wxg: Crystal structure of CYLD USP domain (C596A) in complex with Lys6... -

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Basic information

Entry
Database: PDB / ID: 3wxg
TitleCrystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin
Components
  • (Ubiquitin) x 2
  • 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 / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism ...Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / Ub-specific processing proteases / protein linear deubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Regulation of BACH1 activity / regulation of intrinsic apoptotic signaling pathway / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / central nervous system morphogenesis / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of innate immune responses to cytosolic DNA / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / Dual Incision in GG-NER / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TNFR1-induced NF-kappa-B signaling pathway / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / Dual incision in TC-NER / Inactivation of CSF3 (G-CSF) signaling / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Oncogene Induced Senescence / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IKK complex recruitment mediated by RIP1 / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Deactivation of the beta-catenin transactivating complex
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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Ubiquitin
C: Ubiquitin
D: Uncharacterized protein
E: Ubiquitin
F: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)105,5456
Polymers105,5456
Non-polymers00
Water00
1
A: Uncharacterized protein
B: Ubiquitin
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)52,7733
Polymers52,7733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Uncharacterized protein
E: Ubiquitin
F: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)52,7733
Polymers52,7733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.017, 65.657, 69.821
Angle α, β, γ (deg.)103.49, 89.86, 90.61
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C
13B
23E
14B
24F
15C
25E
16C
26F
17E
27F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA577 - 8853 - 311
21TYRTYRDD577 - 8853 - 311
12LEULEUBB1 - 711 - 71
22LEULEUCC1 - 711 - 71
13GLYGLYBB1 - 761 - 76
23GLYGLYEE1 - 761 - 76
14LEULEUBB1 - 711 - 71
24LEULEUFF1 - 711 - 71
15LEULEUCC1 - 711 - 71
25LEULEUEE1 - 711 - 71
16ARGARGCC1 - 721 - 72
26ARGARGFF1 - 721 - 72
17LEULEUEE1 - 711 - 71
27LEULEUFF1 - 711 - 71

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein Uncharacterized protein / CYLD protein


Mass: 35975.520 Da / Num. of mol.: 2 / Fragment: USP domain, UNP residues 578-780, Linker, 850-951 / Mutation: C596A, 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 / distal ubiquitin


Mass: 8604.845 Da / Num. of mol.: 2 / Mutation: K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubc / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0CG50
#3: Protein Ubiquitin / proximal ubiquitin


Mass: 8192.375 Da / Num. of mol.: 2 / Fragment: UNP residues 1-72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubc / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0CG50

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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: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M sodium malonate buffer, 18% PEG3350, pH 7.0, 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: Jun 28, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 15888 / Num. obs: 15888 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Rsym value: 0.101
Reflection shellResolution: 3.1→3.15 Å / Mean I/σ(I) obs: 2.06 / Rsym value: 0.399 / % possible all: 91.8

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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: 3.1→41.89 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / SU B: 57.635 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.554 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24559 758 5 %RANDOM
Rwork0.18816 ---
obs0.19098 14407 96.7 %-
all-15888 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.137 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å2-0.87 Å2-0.32 Å2
2--3.88 Å20.56 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 3.1→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7218 0 0 0 7218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197352
X-RAY DIFFRACTIONr_bond_other_d0.0030.027166
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9819908
X-RAY DIFFRACTIONr_angle_other_deg0.869316544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6825888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73124.529340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.6151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6551544
X-RAY DIFFRACTIONr_chiral_restr0.070.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218142
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021624
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_it2.7034.8633576
X-RAY DIFFRACTIONr_mcbond_other2.7044.8633575
X-RAY DIFFRACTIONr_mcangle_it4.5737.2884456
X-RAY DIFFRACTIONr_mcangle_other4.5727.2894457
X-RAY DIFFRACTIONr_scbond_it2.6815.1713776
X-RAY DIFFRACTIONr_scbond_other2.685.1723777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5827.6185453
X-RAY DIFFRACTIONr_long_range_B_refined7.49437.8388425
X-RAY DIFFRACTIONr_long_range_B_other7.49437.848426
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A192630.06
12D192630.06
21B45110.08
22C45110.08
31B48450.06
32E48450.06
41B45100.08
42F45100.08
51C45350.07
52E45350.07
61C47670.07
62F47670.07
71E45330.07
72F45330.07
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 58 -
Rwork0.286 1049 -
obs--93.34 %
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)
11.00230.10610.04690.20680.03190.3838-0.0801-0.1462-0.1037-0.06480.0192-0.0432-0.0481-0.0340.06090.0760.04180.04360.09810.0280.0503-1.55741.94325.3962
21.6927-0.8486-2.40264.91780.69993.46970.121-0.2907-0.2347-0.2018-0.44420.2717-0.12040.47680.32310.0724-0.0174-0.04630.14110.01410.1023.3858-21.8078-1.96
32.685-0.2217-0.18823.9357-0.62493.0991-0.2873-0.2005-0.1735-0.42050.2494-0.24660.107-0.39420.03790.0819-0.00890.04880.0795-0.00230.02932.158512-22.9487
41.2-0.1358-0.18160.1818-0.0570.518-0.12930.15390.08620.08480.0299-0.05290.0133-0.02830.09950.0754-0.0332-0.040.07950.02430.0465-26.699536.508-32.9532
50.05020.1820.3596.16430.8093.4790.01040.0366-0.0009-0.0858-0.19440.1089-0.35350.2810.18390.15030.0094-0.08020.0474-0.00970.0436-21.876660.4154-25.5162
63.2413-1.0593-0.01673.5997-0.23112.3339-0.05380.24130.10940.30060.0725-0.0938-0.1465-0.2074-0.01870.07190.0487-0.04450.0625-0.0210.0431-22.77726.4244-4.6247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A577 - 885
2X-RAY DIFFRACTION2B1 - 76
3X-RAY DIFFRACTION3C1 - 72
4X-RAY DIFFRACTION4D577 - 885
5X-RAY DIFFRACTION5E1 - 76
6X-RAY DIFFRACTION6F1 - 72

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