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- PDB-5txk: CRYSTAL STRUCTURE OF USP35 C450S IN COMPLEX WITH UBIQUITIN -

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Basic information

Entry
Database: PDB / ID: 5txk
TitleCRYSTAL STRUCTURE OF USP35 C450S IN COMPLEX WITH UBIQUITIN
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 35,Ubiquitin carboxyl-terminal hydrolase 35
KeywordsHYDROLASE / Deubiquitinase
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / 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 POLK / neuron projection morphogenesis / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN
Similarity search - Function
: / Ubiquitin carboxyl-terminal hydrolase 38-like, N-terminal domain / : / 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. ...: / Ubiquitin carboxyl-terminal hydrolase 38-like, N-terminal domain / : / 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. / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin B / Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.84 Å
AuthorsBader, G. / Weiss-Puxbaum, A. / Zoephel, A.
CitationJournal: J. Cell. Sci. / Year: 2018
Title: Expansion of DUB functionality generated by alternative isoforms - USP35, a case study.
Authors: Leznicki, P. / Natarajan, J. / Bader, G. / Spevak, W. / Schlattl, A. / Abdul Rehman, S.A. / Pathak, D. / Weidlich, S. / Zoephel, A. / Bordone, M.C. / Barbosa-Morais, N.L. / Boehmelt, G. / Kulathu, Y.
History
DepositionNov 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 35,Ubiquitin carboxyl-terminal hydrolase 35
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8569
Polymers50,3162
Non-polymers5407
Water12,304683
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-38 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.235, 104.235, 106.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1406-

HOH

21A-1632-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ubiquitin carboxyl-terminal hydrolase 35,Ubiquitin carboxyl-terminal hydrolase 35 / Deubiquitinating enzyme 35 / Ubiquitin thioesterase 35 / Ubiquitin-specific-processing protease 35


Mass: 41739.152 Da / Num. of mol.: 1 / Fragment: UNP residues 432-603,UNP residues 754-944
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP35, KIAA1372, USP34 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P2H5, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39, UniProt: P0CG47*PLUS

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Non-polymers , 4 types, 690 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.95 M ammonium sulphate 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.84→47.38 Å / Num. obs: 51309 / % possible obs: 100 % / Redundancy: 37.4 % / Net I/σ(I): 37

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Processing

Software
NameVersionClassification
BUSTER-TNT2.11.6refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84→47.38 Å / Cor.coef. Fo:Fc: 0.9577 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.1834 1983 3.86 %RANDOM
Rwork0.1602 ---
obs0.1611 51309 99.87 %-
Displacement parametersBiso max: 123.55 Å2 / Biso mean: 25.24 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.7062 Å20 Å20 Å2
2---0.7062 Å20 Å2
3---1.4125 Å2
Refine analyzeLuzzati coordinate error obs: 0.174 Å
Refinement stepCycle: final / Resolution: 1.84→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 28 683 3842
Biso mean--37.5 42.28 -
Num. residues----392
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1150SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes470HARMONIC5
X-RAY DIFFRACTIONt_it3263HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4311SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3263HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4410HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion15.89
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2286 142 3.8 %
Rwork0.2081 3599 -
all0.2089 3741 -
obs--99.87 %
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)
10.85320.0342-0.11940.9156-0.12450.93320.0068-0.0210.04580.0888-0.0402-0.1049-0.13110.16960.0334-0.021-0.0345-0.0192-0.02760.0196-0.035778.730379.72739.4504
20.7708-0.9235-0.36311.67512.12925.7572-0.172-0.17780.01560.23960.1050.0386-0.0266-0.12010.0670.00990.00520.0098-0.01910.0178-0.028565.053879.22452.3057
30.8301-0.0298-0.00830.09380.07080.0385-0.0501-0.15830.0863-0.0054-0.01240.038-0.0817-0.07810.0626-0.012-0.0088-0.0026-0.004-0.0046-0.011247.625581.490542.5923
40.95110.1735-0.38820.3483-0.09350.366-0.0580.16060.0615-0.05130.02650.025-0.004-0.0790.0315-0.0008-0.0237-0.0152-0.00760.0081-0.036959.152578.12526.7782
52.5010.535-0.11950.2156-0.06051.0366-0.0915-0.034-0.11220.07170.01340.02470.2352-0.14030.0781-0.0137-0.00020.0379-0.0124-0.0325-0.009645.842264.72939.2932
61.59110.112-0.53063.9619-0.71620.8944-0.0321-0.0498-0.15510.08310.08350.0480.1527-0.0185-0.0514-0.0279-0.02630.014-0.0187-0.01370.017554.114759.128437.1316
73.6730.0514-0.8720.02690.41353.59650.0583-0.28690.09010.1848-0.0293-0.11620.06670.0851-0.0290.01760.00040.008-0.0046-0.0152-0.02557.071967.133446.2282
81.7872-0.0243-0.84950.5165-0.12411.4067-0.0876-0.1182-0.02190.1226-0.00770.0301-0.0925-0.08030.09530.00830.00470.0023-0.0073-0.0153-0.003854.738668.103440.3222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|434 - A|520 }A434 - 520
2X-RAY DIFFRACTION2{ A|521 - A|550 }A521 - 550
3X-RAY DIFFRACTION3{ A|551 - A|593 }A551 - 593
4X-RAY DIFFRACTION4{ A|594 - A|927 }A594 - 927
5X-RAY DIFFRACTION5{ B|1 - B|22 }B1 - 22
6X-RAY DIFFRACTION6{ B|23 - B|44 }B23 - 44
7X-RAY DIFFRACTION7{ B|45 - B|56 }B45 - 56
8X-RAY DIFFRACTION8{ B|57 - B|76 }B57 - 76

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