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- PDB-8c61: Structure of USP54 in complex with Lys63-linked diUbiquitin-PA -

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Basic information

Entry
Database: PDB / ID: 8c61
TitleStructure of USP54 in complex with Lys63-linked diUbiquitin-PA
Components
  • Inactive ubiquitin carboxyl-terminal hydrolase 54
  • Polyubiquitin-B
  • Ubiquitin
KeywordsHYDROLASE / USP / USP54 / Ubiquitin / DUB / DUBs / Deubiquitinase / K63 / Lys63
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / protein deubiquitination / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis
Similarity search - Function
: / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Tail fiber / Ubiquitin carboxyl-terminal hydrolase 54
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWendrich, K. / Gersch, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck SocietyCGC-III-352S Germany
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53.
Authors: Wendrich, K. / Gallant, K. / Recknagel, S. / Petroulia, S. / Kazi, N.H. / Hane, J.A. / Fuhrer, S. / Bezstarosti, K. / O'Dea, R. / Demmers, J. / Gersch, M.
History
DepositionJan 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inactive ubiquitin carboxyl-terminal hydrolase 54
B: Polyubiquitin-B
C: Ubiquitin
D: Inactive ubiquitin carboxyl-terminal hydrolase 54
E: Polyubiquitin-B
F: Ubiquitin
G: Inactive ubiquitin carboxyl-terminal hydrolase 54
H: Polyubiquitin-B
I: Ubiquitin
J: Inactive ubiquitin carboxyl-terminal hydrolase 54
K: Polyubiquitin-B
L: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,78732
Polymers227,65712
Non-polymers1,13020
Water3,837213
1
A: Inactive ubiquitin carboxyl-terminal hydrolase 54
B: Polyubiquitin-B
C: Ubiquitin
D: Inactive ubiquitin carboxyl-terminal hydrolase 54
E: Polyubiquitin-B
F: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,42917
Polymers113,8296
Non-polymers60111
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Inactive ubiquitin carboxyl-terminal hydrolase 54
H: Polyubiquitin-B
I: Ubiquitin
J: Inactive ubiquitin carboxyl-terminal hydrolase 54
K: Polyubiquitin-B
L: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,35815
Polymers113,8296
Non-polymers5309
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.743, 126.559, 144.167
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

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Protein , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
Inactive ubiquitin carboxyl-terminal hydrolase 54 / Inactive ubiquitin-specific peptidase 54


Mass: 39789.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP54, C10orf29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70EL1
#2: Protein
Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Protein
Ubiquitin


Mass: 8604.845 Da / Num. of mol.: 4 / Mutation: K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 5 types, 233 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 27.2 % (v/v) PEG 400, 0.1 M HEPES, 0.2 M calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→63.28 Å / Num. obs: 149985 / % possible obs: 99.96 % / Redundancy: 8.9 % / Biso Wilson estimate: 74.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.066 / Net I/σ(I): 16.2
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 1.239 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7759 / CC1/2: 0.682 / Rrim(I) all: 1.313

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALS3.5.0data reduction
Aimless1.12.10data scaling
CRANK22.0.281phasing
Coot0.7.1model building
PHASER2.8.3phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→63.28 Å / SU ML: 0.4309 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.968
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2433 7383 4.92 %
Rwork0.2004 142602 -
obs0.2026 149985 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.94 Å2
Refinement stepCycle: LAST / Resolution: 2.5→63.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14636 0 32 213 14881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004414936
X-RAY DIFFRACTIONf_angle_d0.622820230
X-RAY DIFFRACTIONf_chiral_restr0.04462342
X-RAY DIFFRACTIONf_plane_restr0.00392608
X-RAY DIFFRACTIONf_dihedral_angle_d18.57285380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.49772950.38614749X-RAY DIFFRACTION99.88
2.53-2.560.51692450.37574801X-RAY DIFFRACTION99.96
2.56-2.590.39042800.36574699X-RAY DIFFRACTION99.98
2.59-2.620.37942190.33834744X-RAY DIFFRACTION99.94
2.62-2.660.3662410.31364735X-RAY DIFFRACTION99.94
2.66-2.690.39262410.30024736X-RAY DIFFRACTION99.86
2.69-2.730.30572740.28124758X-RAY DIFFRACTION99.92
2.73-2.770.3442800.28124712X-RAY DIFFRACTION99.92
2.77-2.820.30512590.27274767X-RAY DIFFRACTION99.94
2.82-2.860.34352500.25964763X-RAY DIFFRACTION99.98
2.86-2.910.31232370.25914759X-RAY DIFFRACTION99.98
2.91-2.960.30362100.27324774X-RAY DIFFRACTION100
2.96-3.020.34332380.27794734X-RAY DIFFRACTION99.82
3.02-3.080.30762060.28844809X-RAY DIFFRACTION99.84
3.08-3.150.38422400.28634773X-RAY DIFFRACTION99.98
3.15-3.220.34452110.27564775X-RAY DIFFRACTION100
3.22-3.30.31082720.25194712X-RAY DIFFRACTION99.98
3.3-3.390.26932680.2314747X-RAY DIFFRACTION99.98
3.39-3.490.27392380.23594756X-RAY DIFFRACTION100
3.49-3.610.27162640.21984778X-RAY DIFFRACTION99.98
3.61-3.730.26532300.20674768X-RAY DIFFRACTION100
3.73-3.880.2092210.2084761X-RAY DIFFRACTION100
3.88-4.060.28852320.19294765X-RAY DIFFRACTION100
4.06-4.270.21652670.16434746X-RAY DIFFRACTION99.96
4.27-4.540.2012190.15564765X-RAY DIFFRACTION99.62
4.54-4.890.1762210.14284787X-RAY DIFFRACTION100
4.89-5.380.22582720.16554708X-RAY DIFFRACTION100
5.39-6.160.22712550.17544759X-RAY DIFFRACTION100
6.16-7.760.20022890.18214703X-RAY DIFFRACTION99.98
7.76-63.280.15712090.15524759X-RAY DIFFRACTION99

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