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- PDB-7p99: Structure of human USPL1 in complex with SUMO2 -

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Basic information

Entry
Database: PDB / ID: 7p99
TitleStructure of human USPL1 in complex with SUMO2
Components
  • SUMO-specific isopeptidase USPL1
  • Small ubiquitin-related modifier
KeywordsHYDROLASE / USPL1 / SUMO2
Function / homology
Function and homology information


Cajal body organization / snRNA transcription / deSUMOylase activity / protein desumoylation / SUMO binding / Cajal body / cell population proliferation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular space / nucleus
Similarity search - Function
Ubiquitin-specific peptidase-like, SUMO isopeptidase / Domain of unknown function DUF4650 / USPL1 peptidase / Ubiquitin-specific peptidase-like, SUMO isopeptidase / Domain of unknown function (DUF4650) / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily ...Ubiquitin-specific peptidase-like, SUMO isopeptidase / Domain of unknown function DUF4650 / USPL1 peptidase / Ubiquitin-specific peptidase-like, SUMO isopeptidase / Domain of unknown function (DUF4650) / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Small ubiquitin-related modifier / SUMO-specific isopeptidase USPL1
Similarity search - Component
Biological speciesHomo sapiens (human)
Peromyscus maniculatus bairdii (prairie deer mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsReverter, D. / Ying, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for the SUMO protease activity of the atypical ubiquitin-specific protease USPL1.
Authors: Li, Y. / Varejao, N. / Reverter, D.
History
DepositionJul 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUMO-specific isopeptidase USPL1
C: Small ubiquitin-related modifier
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2473
Polymers50,1812
Non-polymers651
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-10 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.709, 69.884, 53.643
Angle α, β, γ (deg.)90.000, 90.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SUMO-specific isopeptidase USPL1 / Ubiquitin-specific peptidase-like protein 1 / USP-like 1


Mass: 38686.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USPL1, C13orf22, D13S106 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5W0Q7, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Small ubiquitin-related modifier / SUMO


Mass: 11494.796 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Point mutant C54S and G93A
Source: (gene. exp.) Peromyscus maniculatus bairdii (prairie deer mouse)
Gene: Sumo2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6J0CIQ7
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.89 Å3/Da / Density % sol: 35.05 %
Crystal growTemperature: 311 K / Method: vapor diffusion, hanging drop
Details: 0.2M Potassium thiocyanate, 0.1M Sodium Acetate pH 5.0, 8% PEG20000, 8% PEG500MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.799→41.041 Å / Num. obs: 33606 / % possible obs: 96.5 % / Redundancy: 2.5 % / CC1/2: 0.993 / Net I/σ(I): 7.8
Reflection shellResolution: 1.799→1.83 Å / Num. unique obs: 1664 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
AutoProcessdata reduction
AutoProcessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALPHAFOLD

Resolution: 1.8→41.04 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 1620 4.83 %
Rwork0.1745 31920 -
obs0.1756 33540 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.67 Å2 / Biso mean: 33.986 Å2 / Biso min: 14.14 Å2
Refinement stepCycle: final / Resolution: 1.8→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 1 176 3000
Biso mean--24.22 38.29 -
Num. residues----345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.850.27081660.24572648281498
1.85-1.910.23481550.21562672282797
1.91-1.980.22551290.19382641277097
1.98-2.060.23491300.19242727285798
2.06-2.150.23951180.18552698281698
2.15-2.270.2131360.18282659279597
2.27-2.410.2381430.18142669281297
2.41-2.60.22531300.18162667279797
2.6-2.860.22591300.18322663279396
2.86-3.270.17161330.17542644277796
3.27-4.120.18511320.15332646277895
4.12-41.040.14761180.16032586270491
Refinement TLS params.Method: refined / Origin x: 19.3362 Å / Origin y: 7.6516 Å / Origin z: -1.9001 Å
111213212223313233
T0.1791 Å20.0132 Å2-0.0184 Å2-0.1186 Å2-0.0178 Å2--0.1661 Å2
L2.7972 °20.2709 °2-0.454 °2-0.754 °2-0.2637 °2--0.8902 °2
S0.0065 Å °0.1141 Å °-0.0004 Å °0.0104 Å °0.0114 Å °0.0904 Å °-0.0567 Å °-0.0989 Å °-0.0285 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA225 - 601
2X-RAY DIFFRACTION1allC17 - 95
3X-RAY DIFFRACTION1allS1 - 176

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