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- PDB-7zjv: Structure of human USPL1 in covalent complex with DeltaN-SUMO2/3-... -

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Basic information

Entry
Database: PDB / ID: 7zjv
TitleStructure of human USPL1 in covalent complex with DeltaN-SUMO2/3-PA probe
Components
  • SUMO-specific isopeptidase USPL1
  • Small ubiquitin-related modifier 2
KeywordsHYDROLASE / USP / SUMO / Ubiquitin / probe / ubiquitin-like modifier
Function / homology
Function and homology information


snRNA transcription / Cajal body organization / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMO binding / SUMOylation of SUMOylation proteins ...snRNA transcription / Cajal body organization / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMO binding / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / Cajal body / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of intracellular receptors / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / cell population proliferation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / ubiquitin protein ligase binding / proteolysis / RNA binding / extracellular space / nucleoplasm / 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 domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Small ubiquitin-related modifier 2 / SUMO-specific isopeptidase USPL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhao, Z. / Gersch, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
Citation
Journal: J.Am.Chem.Soc. / Year: 2023
Title: Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases.
Authors: Zhao, Z. / O'Dea, R. / Wendrich, K. / Kazi, N. / Gersch, M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Database references / Category: 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: SUMO-specific isopeptidase USPL1
B: Small ubiquitin-related modifier 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2739
Polymers41,9732
Non-polymers3007
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, A,B
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-48 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.708, 95.708, 82.880
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

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Protein , 2 types, 2 molecules AB

#1: Protein SUMO-specific isopeptidase USPL1


Mass: 33203.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USPL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5W0Q7
#2: Protein Small ubiquitin-related modifier 2 / SUMO-2 / HSMT3 / SMT3 homolog 2 / SUMO-3 / Sentrin-2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 8769.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO2, SMT3B, SMT3H2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61956

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Non-polymers , 4 types, 35 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.9 / Details: 100 mM CHES pH 8.9, 34% PEG600

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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 EIGER2 X 16M / Detector: PIXEL / Date: Jun 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→42.8 Å / Num. obs: 28746 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 76.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.057 / Net I/σ(I): 18.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1597 / CC1/2: 0.718 / Rrim(I) all: 0.933

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia20.5.902data reduction
DIALS1.14.13data collection
PHASER2.8.3phasing
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZJU

7zju


Resolution: 2.4→42.8 Å / SU ML: 0.4606 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.2751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 1430 4.97 %
Rwork0.2301 27316 -
obs0.2316 28746 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 10 28 2659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542690
X-RAY DIFFRACTIONf_angle_d1.13343661
X-RAY DIFFRACTIONf_chiral_restr0.07406
X-RAY DIFFRACTIONf_plane_restr0.0065476
X-RAY DIFFRACTIONf_dihedral_angle_d23.1586928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.4291550.35842713X-RAY DIFFRACTION99.69
2.49-2.590.39111320.34542770X-RAY DIFFRACTION99.97
2.59-2.70.46791230.32572725X-RAY DIFFRACTION99.96
2.7-2.850.41221520.32752701X-RAY DIFFRACTION99.96
2.85-3.020.3421430.29472736X-RAY DIFFRACTION100
3.02-3.260.32111300.29092760X-RAY DIFFRACTION100
3.26-3.580.26581450.24632730X-RAY DIFFRACTION100
3.59-4.10.23441260.22122752X-RAY DIFFRACTION100
4.11-5.170.19831660.19022695X-RAY DIFFRACTION100
5.17-42.80.25431580.20362734X-RAY DIFFRACTION100
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)
11.974745780881.057814209031.649397812165.22814463611.295415775043.22129877767-0.656155468453-0.04793091983380.9190860645361.24503909511-0.44890822281-1.01654949328-1.874387010211.244115617760.7074021599971.57664894797-0.199315391717-0.7109627671450.8965374431840.1489596915321.1866251107836.731137917222.34312390427.0493539831
24.6598133825-1.925558326134.086501156083.89108955071-2.373662516749.42351617840.20197485767-0.316197322379-0.5630359329820.2215354017190.1535003766840.286415326864-0.098496338081-0.459974334613-0.3003298977950.6435662723980.0489782374329-0.1089918981120.50167291530.1226555325930.79334822741921.915011624311.87438098714.3403684388
35.02832716757-4.874237102680.4738761864297.553632936164.511409956059.23350085711-0.506413245372-0.232882355819-1.34323356221.476277410190.222658130799-0.845146829060.515246970338-0.4875430018320.3491667496961.162509986920.42478809194-0.1831863500590.732238552812-0.07156650300261.176954054637.7209401257-1.02659789676-4.03281179839
46.99867949313-2.92393264824-5.736702276922.273986015082.553739016134.544913982821.135518587923.439727075-0.606406321095-1.00476170953-1.43372707643-0.626849569488-1.37435360287-0.354172904860.4142103273021.256886178380.373747847662-0.007015706395271.690461372440.06233696199220.88626895938137.60928675731.82756765305-4.84381037469
56.899686079514.524057345450.3851407181765.570662440822.647035613273.79699979744-0.04574006921991.57961852335-0.112110058933-0.621540797824-0.1316074360450.1185424652090.9185363132642.289501986340.2242068388080.7938963159930.316223977999-0.1242733247461.434128165170.1745803085560.84133340656934.90241913119.74005978102-3.46184308515
68.10877444086-2.28933649523-5.296749351916.104094389814.684689429736.237415334960.03161386165641.13090979677-0.142699689539-1.01607418822-0.228880554208-0.2660007995580.2718485707570.7278754420990.2372717326740.9225761976020.267792900593-0.08029544322261.262097834780.07844629416910.81425444729539.83527974767.121303147861.30823807579
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 225 through 323 )AA225 - 3231 - 83
22chain 'A' and (resid 324 through 500 )AA324 - 50084 - 260
33chain 'B' and (resid 16 through 23 )BC16 - 231 - 8
44chain 'B' and (resid 24 through 38 )BC24 - 389 - 23
55chain 'B' and (resid 39 through 66 )BC39 - 6624 - 51
66chain 'B' and (resid 67 through 91 )BC67 - 9152 - 76

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