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- PDB-8iya: Complex of SETDB1-derived peptide bound to UBE2E1 -

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Basic information

Entry
Database: PDB / ID: 8iya
TitleComplex of SETDB1-derived peptide bound to UBE2E1
Components
  • Histone-lysine N-methyltransferase SETDB1
  • Ubiquitin-conjugating enzyme E2 E1
KeywordsPROTEIN BINDING / Ubiquitin / Recognition / Conjugation
Function / homology
Function and homology information


ISG15 transferase activity / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / ISG15-protein conjugation / positive regulation of DNA methylation-dependent heterochromatin formation / heterochromatin organization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity ...ISG15 transferase activity / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / ISG15-protein conjugation / positive regulation of DNA methylation-dependent heterochromatin formation / heterochromatin organization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / ubiquitin ligase complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / promoter-specific chromatin binding / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / CDK-mediated phosphorylation and removal of Cdc6 / ISG15 antiviral mechanism / PKMTs methylate histone lysines / protein polyubiquitination / ubiquitin-protein transferase activity / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / chromosome / methylation / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / protein ubiquitination / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / : / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / Pre-SET domain ...Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / : / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Tudor domain / Tudor domain / Post-SET domain / Post-SET domain profile. / Methyl-CpG binding domain / Methyl-CpG DNA binding / Ubiquitin-conjugating enzyme, active site / Methyl-CpG binding domain / Ubiquitin-conjugating (UBC) active site signature. / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / Ubiquitin-conjugating enzyme/RWD-like / SET domain profile. / SET domain
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 E1 / Histone-lysine N-methyltransferase SETDB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsDu, Y.X. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810 China
CitationJournal: To Be Published
Title: Complex of SETDB1-derived peptide bound to UBE2E1
Authors: Wu, X.W. / Du, Y.X. / Liu, L.
History
DepositionApr 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ubiquitin-conjugating enzyme E2 E1
A: Ubiquitin-conjugating enzyme E2 E1
C: Ubiquitin-conjugating enzyme E2 E1
D: Histone-lysine N-methyltransferase SETDB1
E: Histone-lysine N-methyltransferase SETDB1
F: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9609
Polymers59,6726
Non-polymers2883
Water64936
1
B: Ubiquitin-conjugating enzyme E2 E1
D: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9873
Polymers19,8912
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-22 kcal/mol
Surface area9110 Å2
MethodPISA
2
A: Ubiquitin-conjugating enzyme E2 E1
E: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9873
Polymers19,8912
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-25 kcal/mol
Surface area9000 Å2
MethodPISA
3
C: Ubiquitin-conjugating enzyme E2 E1
F: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9873
Polymers19,8912
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-23 kcal/mol
Surface area8420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.747, 50.077, 109.248
Angle α, β, γ (deg.)90.000, 91.754, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 E1 / (E3-independent) E2 ubiquitin-conjugating enzyme E1 / E2 ubiquitin-conjugating enzyme E1 / UbcH6 / ...(E3-independent) E2 ubiquitin-conjugating enzyme E1 / E2 ubiquitin-conjugating enzyme E1 / UbcH6 / Ubiquitin carrier protein E1 / Ubiquitin-protein ligase E1


Mass: 19203.832 Da / Num. of mol.: 3 / Mutation: C67S, C122P, C153S, C159P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E1, UBCH6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: P51965, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein/peptide Histone-lysine N-methyltransferase SETDB1 / ERG-associated protein with SET domain / ESET / Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 ...ERG-associated protein with SET domain / ESET / Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 / Lysine N-methyltransferase 1E / SET domain bifurcated 1


Mass: 686.689 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, ESET, KIAA0067, KMT1E / Production host: Escherichia coli (E. coli)
References: UniProt: Q15047, [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.0 M Lithium sulfate, 0.1 M MES pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.43→109.2 Å / Num. obs: 21079 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 48.58 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.067 / Rrim(I) all: 0.148 / Net I/σ(I): 7
Reflection shellResolution: 2.43→2.57 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 14473 / CC1/2: 0.877 / Rpim(I) all: 0.311 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.7data scaling
PHENIX1.19.2_4158phasing
Aimless0.7.7data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→41.42 Å / SU ML: 0.2773 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.9187
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2472 1045 4.96 %
Rwork0.2047 20025 -
obs0.2069 21070 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.92 Å2
Refinement stepCycle: LAST / Resolution: 2.43→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 15 36 3913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00953977
X-RAY DIFFRACTIONf_angle_d1.13585425
X-RAY DIFFRACTIONf_chiral_restr0.0616602
X-RAY DIFFRACTIONf_plane_restr0.0085698
X-RAY DIFFRACTIONf_dihedral_angle_d17.35821484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.560.31011660.26742809X-RAY DIFFRACTION99.73
2.56-2.720.30171370.25132866X-RAY DIFFRACTION99.9
2.72-2.930.31771430.24152854X-RAY DIFFRACTION99.93
2.93-3.230.34271640.24342818X-RAY DIFFRACTION99.8
3.23-3.690.28781320.22342875X-RAY DIFFRACTION99.77
3.7-4.650.20161360.17812883X-RAY DIFFRACTION99.37
4.65-41.420.1941670.17562920X-RAY DIFFRACTION98.75

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