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- PDB-8bs3: Structure of USP36 in complex with Fubi-PA -

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Basic information

Entry
Database: PDB / ID: 8bs3
TitleStructure of USP36 in complex with Fubi-PA
Components
  • 40S ribosomal protein S30
  • Ubiquitin carboxyl-terminal hydrolase 36
KeywordsHYDROLASE / USP / USP36 / Ubiquitin / Fubi / S30 / Fau / probe
Function / homology
Function and homology information


regulation of rRNA processing / regulation of autophagy of mitochondrion / nucleolus organization / K48-linked deubiquitinase activity / Formation of the ternary complex, and subsequently, the 43S complex / positive regulation of protein targeting to mitochondrion / Ribosomal scanning and start codon recognition / Translation initiation complex formation / negative regulation of macroautophagy / protein deubiquitination ...regulation of rRNA processing / regulation of autophagy of mitochondrion / nucleolus organization / K48-linked deubiquitinase activity / Formation of the ternary complex, and subsequently, the 43S complex / positive regulation of protein targeting to mitochondrion / Ribosomal scanning and start codon recognition / Translation initiation complex formation / negative regulation of macroautophagy / protein deubiquitination / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / innate immune response in mucosa / regulation of protein stability / Regulation of expression of SLITs and ROBOs / antimicrobial humoral immune response mediated by antimicrobial peptide / chromatin organization / small ribosomal subunit / antibacterial humoral response / ubiquitin-dependent protein catabolic process / SARS-CoV-2 modulates host translation machinery / regulation of apoptotic process / cytosolic small ribosomal subunit / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cytoplasmic translation / protein stabilization / defense response to Gram-positive bacterium / nuclear speck / structural constituent of ribosome / translation / cysteine-type endopeptidase activity / nucleolus / RNA binding / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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-like protein FUBI / Ribosomal protein S30 / Ribosomal protein S30 ...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-like protein FUBI / Ribosomal protein S30 / Ribosomal protein S30 / 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
Similarity search - Domain/homology
prop-2-en-1-amine / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Ubiquitin carboxyl-terminal hydrolase 36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsO'Dea, R. / Gersch, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck SocietyCGC-III-352S Germany
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Molecular basis for ubiquitin/Fubi cross-reactivity in USP16 and USP36.
Authors: O'Dea, R. / Kazi, N. / Hoffmann-Benito, A. / Zhao, Z. / Recknagel, S. / Wendrich, K. / Janning, P. / Gersch, M.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 15, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 36
B: 40S ribosomal protein S30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6775
Polymers50,4892
Non-polymers1883
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-12 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.626, 75.892, 96.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 36 / Deubiquitinating enzyme 36 / Ubiquitin thioesterase 36 / Ubiquitin-specific-processing protease 36


Mass: 42781.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP36, KIAA1453 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P275, ubiquitinyl hydrolase 1
#2: Protein 40S ribosomal protein S30 / Small ribosomal subunit protein eS30


Mass: 7707.741 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAU / Production host: Escherichia coli (E. coli) / References: UniProt: P62861
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MMT buffer pH 7.0, 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91883 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91883 Å / Relative weight: 1
ReflectionResolution: 2.2→59.63 Å / Num. obs: 45243 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 24.1 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.177 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2 / Num. unique obs: 4527 / CC1/2: 0.505 / % possible all: 99.8

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Processing

Software
NameVersionClassification
xia23.6.1data reduction
PHENIX1.19.2_4158refinement
DIALS3.6.2data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→59.63 Å / SU ML: 0.2221 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9068
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2272 2256 4.99 %
Rwork0.1956 42974 -
obs0.1972 45230 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→59.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 6 269 3342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213143
X-RAY DIFFRACTIONf_angle_d0.50294263
X-RAY DIFFRACTIONf_chiral_restr0.0388485
X-RAY DIFFRACTIONf_plane_restr0.0029549
X-RAY DIFFRACTIONf_dihedral_angle_d15.48811127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.30181470.27722695X-RAY DIFFRACTION98.78
2.25-2.30.29791800.26462652X-RAY DIFFRACTION98.68
2.3-2.360.30521200.27022721X-RAY DIFFRACTION98.75
2.36-2.420.31041260.25162669X-RAY DIFFRACTION99.18
2.42-2.490.28821270.23942678X-RAY DIFFRACTION98.66
2.49-2.570.30011720.24592659X-RAY DIFFRACTION98.4
2.57-2.670.28811160.23982715X-RAY DIFFRACTION98.64
2.67-2.770.27081550.23372673X-RAY DIFFRACTION98.43
2.77-2.90.24171610.21232686X-RAY DIFFRACTION98.96
2.9-3.050.21691380.19072676X-RAY DIFFRACTION99.22
3.05-3.240.20111370.18232668X-RAY DIFFRACTION98.84
3.24-3.490.21891110.16382725X-RAY DIFFRACTION98.71
3.49-3.840.19491560.15452672X-RAY DIFFRACTION98.43
3.84-4.40.1411330.1412672X-RAY DIFFRACTION98.49
4.4-5.540.19911340.16392727X-RAY DIFFRACTION99.41
5.54-59.630.22171430.21092686X-RAY DIFFRACTION99.02
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)
12.99052371927-0.512427422650.5370622699640.794904639956-0.1877483839661.24173687032-0.0250213313529-0.0768336928278-0.185317018827-0.03278310037780.0368424497720.06680842761380.141079007219-0.0943279535297-0.04117200364640.158197423277-0.0009913111339980.01109674747990.161328247673-0.01429097896490.16535510863-9.5473835784356.65698524328.76050783788
20.5678692166860.0922238514484-0.08038299639752.528066239950.04159884278030.934914816797-0.00495146343011-0.04691658122220.200669664914-0.165856539761-0.0645455949070.0817766566604-0.23712879583-0.06559035357990.06414968712150.2154267034020.0306591465162-0.006064388085520.236127572492-0.03492258397950.246307105738-14.882038956684.20985243492.53753975894
32.07621699544-0.818122315020.2565680877962.21718791538-0.5962770934721.464541622680.0129443770371-0.2821637596020.08006188389540.215474670120.05494248931230.0188535958709-0.2201528261790.0548349368774-0.06200654095390.2114808802470.008820742895330.002853485920220.261438499607-0.08162931084330.120215898568-8.7189856756571.552030676520.2201906646
46.202351403430.694516642205-1.615519402136.876989119120.6386067112791.312986403170.03555808157160.237551384280.349672790562-0.161212975831-0.0802957974854-0.677216656912-0.0926133523137-0.01505308150860.08542382959810.233250624861-0.0107930042853-0.01810774414950.1890303269040.05409939032420.247738230323-0.29666794217182.3795217268-3.50389878075
56.535316004684.23185494211-3.114498819554.92857689265-4.91511842865.5728121494-0.3622763649930.113615413439-0.527726722504-0.8770837585380.0113508449451-0.5045421063010.690029507956-0.1393598737230.3360589710160.4135429693730.01797405739580.04077157664470.170062340379-0.01291477255990.251044603388-3.1818349665971.1882720272-5.57956865654
62.8675907328-2.692264477510.6244030531864.29360095203-1.570643743630.665552832679-0.377960196938-0.1622299025030.290064435911-0.006721939818270.226164795925-0.062559852429-0.252774845959-0.1026255098310.0918508018180.190359752467-0.0281325414755-0.02603199496310.192195591270.006601019937480.229648380204-4.9839920133576.8759814216-1.38636823417
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 101 through 225 )AA101 - 2251 - 125
22chain 'A' and (resid 226 through 319 )AA226 - 319126 - 219
33chain 'A' and (resid 320 through 424 )AA320 - 424220 - 324
44chain 'B' and (resid 1 through 43 )BD1 - 431 - 43
55chain 'B' and (resid 44 through 53 )BD44 - 5344 - 53
66chain 'B' and (resid 54 through 73 )BD54 - 7354 - 73

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