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- PDB-8hfp: Crystal structure of the methyl-CpG-binding domain of SETDB2 in c... -

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Basic information

Entry
Database: PDB / ID: 8hfp
TitleCrystal structure of the methyl-CpG-binding domain of SETDB2 in complex with the cysteine-rich domain of C11orf46 protein
Components
  • ARL14 effector protein
  • Histone-lysine N-methyltransferase SETDB2
KeywordsTRANSCRIPTION / Complex / Zn-binding / Heterochromatin / Histone methylation
Function / homology
Function and homology information


[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 monomethyltransferase activity / heterochromatin organization / left/right axis specification / histone H3K9 methyltransferase activity / histone H3 methyltransferase activity / heart looping / chromosome segregation / PKMTs methylate histone lysines / mitotic cell cycle ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 monomethyltransferase activity / heterochromatin organization / left/right axis specification / histone H3K9 methyltransferase activity / histone H3 methyltransferase activity / heart looping / chromosome segregation / PKMTs methylate histone lysines / mitotic cell cycle / chromosome / methylation / negative regulation of gene expression / cell division / focal adhesion / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
ARL14 effector protein / ARF7 effector protein, C-terminal / ARF7 effector protein C-terminus / : / : / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Methyl-CpG binding domain ...ARL14 effector protein / ARF7 effector protein, C-terminal / ARF7 effector protein C-terminus / : / : / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain
Similarity search - Domain/homology
ARL14 effector protein / Histone-lysine N-methyltransferase SETDB2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMahana, Y. / Ariyoshi, M. / Shirakawa, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K06048 Japan
CitationJournal: Structure / Year: 2024
Title: Structural evidence for protein-protein interaction between the non-canonical methyl-CpG-binding domain of SETDB proteins and C11orf46.
Authors: Mahana, Y. / Ariyoshi, M. / Nozawa, R.S. / Shibata, S. / Nagao, K. / Obuse, C. / Shirakawa, M.
History
DepositionNov 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARL14 effector protein
C: Histone-lysine N-methyltransferase SETDB2
B: ARL14 effector protein
D: Histone-lysine N-methyltransferase SETDB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,93516
Polymers41,9664
Non-polymers96912
Water1,982110
1
A: ARL14 effector protein
C: Histone-lysine N-methyltransferase SETDB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4678
Polymers20,9832
Non-polymers4846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-38 kcal/mol
Surface area8820 Å2
MethodPISA
2
B: ARL14 effector protein
D: Histone-lysine N-methyltransferase SETDB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4678
Polymers20,9832
Non-polymers4846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-60 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.970, 69.970, 116.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ARL14 effector protein / ARF7 effector protein


Mass: 8413.624 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL14EP, ARF7EP, C11orf46 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N8R7
#2: Protein Histone-lysine N-methyltransferase SETDB2 / Chronic lymphocytic leukemia deletion region gene 8 protein / Lysine N-methyltransferase 1F / SET ...Chronic lymphocytic leukemia deletion region gene 8 protein / Lysine N-methyltransferase 1F / SET domain bifurcated 2


Mass: 12569.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB2, C13orf4, CLLD8, KMT1F / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96T68, [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.0 M ammonium sulfate 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→42.06 Å / Num. obs: 30318 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rrim(I) all: 0.098 / Net I/σ(I): 15.8
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1709 / CC1/2: 0.812 / Rpim(I) all: 0.294 / Rrim(I) all: 0.898 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Coot0.9.3model building
BUCCANEER1.6.10model building
SHELXCDphasing
Aimless0.7.4data scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model (SAD-phased)

Resolution: 1.82→42.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.808 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22662 1468 4.8 %RANDOM
Rwork0.18615 ---
obs0.18812 28818 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.278 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.82→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 36 110 2568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132496
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172214
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.6373363
X-RAY DIFFRACTIONr_angle_other_deg1.3751.5855113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0925300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.42522.254142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72615417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3411516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3063.4081218
X-RAY DIFFRACTIONr_mcbond_other3.2923.4051217
X-RAY DIFFRACTIONr_mcangle_it4.6115.0721512
X-RAY DIFFRACTIONr_mcangle_other4.615.0741513
X-RAY DIFFRACTIONr_scbond_it4.3183.8881278
X-RAY DIFFRACTIONr_scbond_other4.213.8491255
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5065.61816
X-RAY DIFFRACTIONr_long_range_B_refined8.41938.1742569
X-RAY DIFFRACTIONr_long_range_B_other8.40438.0582557
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 109 -
Rwork0.252 2039 -
obs--97.06 %

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