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- PDB-6p5l: Crystal Structure of Ubl123 with an EZH2 peptide -

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Basic information

Entry
Database: PDB / ID: 6p5l
TitleCrystal Structure of Ubl123 with an EZH2 peptide
Components
  • PRO-ARG-LYS-LYS-LYS-ARG-LYS-HIS
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / Complex Deubiquitinase / NUCLEAR PROTEIN
Function / homology
Function and homology information


hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / negative regulation of striated muscle cell differentiation / regulation of gliogenesis / negative regulation of keratinocyte differentiation / [histone H3]-lysine27 N-trimethyltransferase / regulation of telomere capping / response to tetrachloromethane / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration ...hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / negative regulation of striated muscle cell differentiation / regulation of gliogenesis / negative regulation of keratinocyte differentiation / [histone H3]-lysine27 N-trimethyltransferase / regulation of telomere capping / response to tetrachloromethane / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of retinoic acid receptor signaling pathway / histone H3K27 trimethyltransferase activity / cerebellar cortex development / primary miRNA binding / histone H3K27 methyltransferase activity / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / positive regulation of cell cycle G1/S phase transition / regulation of retrograde transport, endosome to Golgi / regulatory ncRNA-mediated heterochromatin formation / cardiac muscle hypertrophy in response to stress / negative regulation of stem cell differentiation / facultative heterochromatin formation / DNA alkylation repair / ESC/E(Z) complex / deubiquitinase activity / protein-lysine N-methyltransferase activity / chromatin silencing complex / pronucleus / positive regulation of dendrite development / K48-linked deubiquitinase activity / regulation of tumor necrosis factor-mediated signaling pathway / DNA methylation-dependent constitutive heterochromatin formation / symbiont-mediated disruption of host cell PML body / histone H3 methyltransferase activity / negative regulation of G1/S transition of mitotic cell cycle / G1 to G0 transition / histone methyltransferase activity / synaptic transmission, GABAergic / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / positive regulation of MAP kinase activity / lncRNA binding / positive regulation of protein serine/threonine kinase activity / negative regulation of transcription elongation by RNA polymerase II / Transcriptional Regulation by E2F6 / keratinocyte differentiation / subtelomeric heterochromatin formation / positive regulation of GTPase activity / negative regulation of gluconeogenesis / protein deubiquitination / ribonucleoprotein complex binding / positive regulation of epithelial to mesenchymal transition / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / nucleosome binding / heterochromatin / negative regulation of TORC1 signaling / B cell differentiation / protein localization to chromatin / negative regulation of cytokine production involved in inflammatory response / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / liver regeneration / stem cell differentiation / regulation of signal transduction by p53 class mediator / hippocampus development / transcription corepressor binding / Regulation of PTEN localization / Regulation of PTEN gene transcription / antiviral innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / PRC2 methylates histones and DNA / Defective pyroptosis / G1/S transition of mitotic cell cycle / regulation of protein stability / promoter-specific chromatin binding / chromatin DNA binding / PML body / Negative Regulation of CDH1 Gene Transcription / regulation of circadian rhythm / PKMTs methylate histone lysines / cellular response to hydrogen peroxide / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / HCMV Early Events / p53 binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription corepressor activity / response to estradiol / Regulation of TP53 Degradation / rhythmic process / chromosome / chromatin organization / heterochromatin formation / methylation / histone binding / Oxidative Stress Induced Senescence
Similarity search - Function
EZH2, SET domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain ...EZH2, SET domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase EZH2 / Ubiquitin C-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.296 Å
AuthorsSaridakis, V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106583 Canada
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2.
Authors: Gagarina, V. / Bojagora, A. / Lacdao, I.K. / Luthra, N. / Pfoh, R. / Mohseni, S. / Chaharlangi, D. / Tan, N. / Saridakis, V.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
D: PRO-ARG-LYS-LYS-LYS-ARG-LYS-HIS


Theoretical massNumber of molelcules
Total (without water)84,3853
Polymers84,3853
Non-polymers00
Water00
1
A: Ubiquitin carboxyl-terminal hydrolase 7
D: PRO-ARG-LYS-LYS-LYS-ARG-LYS-HIS


Theoretical massNumber of molelcules
Total (without water)42,7352
Polymers42,7352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 7


Theoretical massNumber of molelcules
Total (without water)41,6501
Polymers41,6501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.452, 165.452, 110.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 41650.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide PRO-ARG-LYS-LYS-LYS-ARG-LYS-HIS


Mass: 1084.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15910*PLUS

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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: 4.5 Å3/Da / Density % sol: 72.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 167 mM NaCl, 20mM Tris, 5mM b-ME, 10mM betaine hydrochlorid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.296→30 Å / Num. obs: 23736 / % possible obs: 99.3 % / Redundancy: 28.9 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.016 / Net I/σ(I): 49.6
Reflection shellResolution: 3.3→3.36 Å / Rmerge(I) obs: 0.94 / Num. unique obs: 2303 / Rpim(I) all: 0.23 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wpi

4wpi


Resolution: 3.296→29.608 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.52
RfactorNum. reflection% reflection
Rfree0.2893 1993 8.43 %
Rwork0.231 --
obs0.2359 23638 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 215.16 Å2 / Biso mean: 122.1608 Å2 / Biso min: 51.58 Å2
Refinement stepCycle: final / Resolution: 3.296→29.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 0 0 5622
Num. residues----687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2962-3.37860.3881390.28281514165399
3.3786-3.46980.45161390.34815011640100
3.4698-3.57170.37921400.299415231663100
3.5717-3.68680.40441420.30551524166699
3.6868-3.81830.34521390.291715101649100
3.8183-3.97080.43821350.31131490162597
3.9708-4.15110.29491420.230615311673100
4.1511-4.36930.27431410.222715341675100
4.3693-4.64210.25841410.190515461687100
4.6421-4.99890.25991440.186915561700100
4.9989-5.49910.20791440.190515601704100
5.4991-6.28820.27741450.234615741719100
6.2882-7.89750.30691480.254516051753100
7.8975-29.60960.25621540.206516771831100

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