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- PDB-7owd: Structure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal spac... -

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Basic information

Entry
Database: PDB / ID: 7owd
TitleStructure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal space group
Components
  • Ubiquitin
  • Ubiquitin carboxyl-terminal hydrolase CYLD
KeywordsIMMUNE SYSTEM / ubiquitin binding domain / deubiquitinating enzyme
Function / homology
Function and homology information


negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / regulation of cilium assembly / negative regulation of p38MAPK cascade / ciliary tip ...negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / regulation of cilium assembly / negative regulation of p38MAPK cascade / ciliary tip / regulation of necroptotic process / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of JNK cascade / regulation of tumor necrosis factor-mediated signaling pathway / proline-rich region binding / positive regulation of extrinsic apoptotic signaling pathway / K48-linked deubiquitinase activity / negative regulation of non-canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / protein K63-linked deubiquitination / positive regulation of T cell differentiation / negative regulation of type I interferon production / K63-linked deubiquitinase activity / positive regulation of T cell receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / necroptotic process / homeostasis of number of cells / protein deubiquitination / positive regulation of protein localization / negative regulation of canonical NF-kappaB signal transduction / 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 / regulation of microtubule cytoskeleton organization / 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 / 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
Similarity search - Function
Phosphorylation region of CYLD, unstructured / CAP Gly-rich-like domain / CAP-Gly domain signature. / 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 ...Phosphorylation region of CYLD, unstructured / CAP Gly-rich-like domain / CAP-Gly domain signature. / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / SH3 type barrels. / : / 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 / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase CYLD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsElliott, P.R. / Komander, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105192732 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R008582/1 United Kingdom
CitationJournal: Cell Rep / Year: 2021
Title: Regulation of CYLD activity and specificity by phosphorylation and ubiquitin-binding CAP-Gly domains.
Authors: Elliott, P.R. / Leske, D. / Wagstaff, J. / Schlicher, L. / Berridge, G. / Maslen, S. / Timmermann, F. / Ma, B. / Fischer, R. / Freund, S.M.V. / Komander, D. / Gyrd-Hansen, M.
History
DepositionJun 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Ubiquitin carboxyl-terminal hydrolase CYLD
A: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,9622
Polymers17,9622
Non-polymers00
Water1,74797
1
B: Ubiquitin carboxyl-terminal hydrolase CYLD


Theoretical massNumber of molelcules
Total (without water)9,3851
Polymers9,3851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,5771
Polymers8,5771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.931, 42.931, 171.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase CYLD / Deubiquitinating enzyme CYLD / Ubiquitin thioesterase CYLD / Ubiquitin-specific-processing protease CYLD


Mass: 9384.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYLD, CYLD1, KIAA0849, HSPC057 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9NQC7, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin / Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 40 (v/v) PEG 300, 100 mM phosphate/citrate pH 4.2

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Data collection

DiffractionMean temperature: 210 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.96863 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.71→41.64 Å / Num. obs: 18356 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 35.32 Å2 / CC1/2: 0.998 / Net I/σ(I): 15
Reflection shellResolution: 1.71→1.74 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 933 / CC1/2: 0.899

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 1IXD

1ubq

1ixd


Resolution: 1.71→41.64 Å / SU ML: 0.2669 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 34.1202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245 886 4.86 %
Rwork0.2136 17351 -
obs0.2151 18237 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.67 Å2
Refinement stepCycle: LAST / Resolution: 1.71→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 0 97 1331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171274
X-RAY DIFFRACTIONf_angle_d1.72391722
X-RAY DIFFRACTIONf_chiral_restr0.078198
X-RAY DIFFRACTIONf_plane_restr0.0109223
X-RAY DIFFRACTIONf_dihedral_angle_d8.8887939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.820.42711600.36682775X-RAY DIFFRACTION99.49
1.82-1.960.33541520.28862839X-RAY DIFFRACTION99.34
1.96-2.150.30031350.23472826X-RAY DIFFRACTION99.56
2.15-2.470.26961530.21532834X-RAY DIFFRACTION99.77
2.47-3.110.24021340.23332950X-RAY DIFFRACTION99.97
3.11-41.640.21851520.19173127X-RAY DIFFRACTION99.91
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)
11.29606463018-0.462622453399-0.7700791084920.568908439295-0.1726820605972.294756573450.03574337741690.0791753370269-0.2127822737880.04503575813860.0847743292002-0.09860209275860.428439182508-0.04860936390370.04669748432330.356069376481-0.0197456026588-0.0165638135090.354658667250.04059937943870.3988763887794.6521.565-21.885
20.79553302303-0.8523820178380.2705148103770.952404637746-0.1371456719040.624290522958-0.08213323748110.1926126579270.08694803047290.0765042499522-0.125288048428-0.0985493279698-0.0300412131820.135240516558-0.06973232111360.339592144318-0.08283044805760.008766194597880.4434631789860.07329685445260.3849161031081.85814.915-39.233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 467:552 )B467 - 552
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1:76 )A1 - 76

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