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- PDB-8t68: Crystal Structure of the SET Domain of Human Histone-Lysine N-Met... -

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Basic information

Entry
Database: PDB / ID: 8t68
TitleCrystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 in complex with RQ3-111
ComponentsHistone-lysine N-methyltransferase KMT5B
KeywordsTRANSPORT PROTEIN / TRANSFERASE/INHIBITOR / SET domain / Methyltransferase / SGC / SUV420H1 / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


[histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / positive regulation of isotype switching / condensed chromosome, centromeric region / S-adenosyl-L-methionine binding / muscle organ development ...[histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / positive regulation of isotype switching / condensed chromosome, centromeric region / S-adenosyl-L-methionine binding / muscle organ development / positive regulation of double-strand break repair via nonhomologous end joining / histone methyltransferase activity / intercellular bridge / PKMTs methylate histone lysines / cytoplasmic ribonucleoprotein granule / fibrillar center / mitotic spindle / microtubule cytoskeleton / methylation / ciliary basal body / cilium / DNA repair / centrosome / chromatin binding / nucleolus / nucleoplasm / metal ion binding / nucleus / plasma membrane
Similarity search - Function
KMT5B , SET domain / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / : / Histone-lysine N-methyltransferase KMT5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZeng, H. / Dong, A. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 in complex with RQ3-111.
Authors: Zeng, H. / Dong, A. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionJun 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase KMT5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4824
Polymers31,6571
Non-polymers8253
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.149, 75.528, 96.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Histone-lysine N-methyltransferase KMT5B / Lysine N-methyltransferase 5B / Lysine-specific methyltransferase 5B / Suppressor of variegation 4- ...Lysine N-methyltransferase 5B / Lysine-specific methyltransferase 5B / Suppressor of variegation 4-20 homolog 1 / Su(var)4-20 homolog 1 / Suv4-20h1 / [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B / [histone H4]-lysine20 N-methyltransferase KMT5B


Mass: 31656.807 Da / Num. of mol.: 1 / Fragment: SET domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT5B, SUV420H1, CGI-85 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4FZB7, [histone H4]-N-methyl-L-lysine20 N-methyltransferase, [histone H4]-lysine20 N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-ZKI / 6,7-dichloro-N-[(3R)-oxolan-3-yl]-4-(pyridin-4-yl)phthalazin-1-amine


Mass: 361.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14Cl2N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% (w/v) PEG3350, 0.2 M MgCl2, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→40.76 Å / Num. obs: 21418 / % possible obs: 99.4 % / Redundancy: 9.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.043 / Rrim(I) all: 0.136 / Χ2: 1.01 / Net I/σ(I): 11.1 / Num. measured all: 202834
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 98.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 1.018 / Num. measured all: 12487 / Num. unique obs: 1318 / CC1/2: 0.798 / Rpim(I) all: 0.344 / Rrim(I) all: 1.076 / Χ2: 0.96 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.256 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26393 1032 4.9 %RANDOM
Rwork0.22578 ---
obs0.22765 19949 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.785 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å2-0 Å2-0 Å2
2---2.19 Å20 Å2
3---3.84 Å2
Refinement stepCycle: 1 / Resolution: 1.9→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 52 67 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181713
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.6432622
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5933970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5055231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74622.661109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76615328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.441512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
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_it2.4292.922933
X-RAY DIFFRACTIONr_mcbond_other2.4272.922933
X-RAY DIFFRACTIONr_mcangle_it3.5114.3611163
X-RAY DIFFRACTIONr_mcangle_other3.5114.3611163
X-RAY DIFFRACTIONr_scbond_it3.0423.2711014
X-RAY DIFFRACTIONr_scbond_other3.0413.271015
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7064.7551460
X-RAY DIFFRACTIONr_long_range_B_refined6.03933.7482150
X-RAY DIFFRACTIONr_long_range_B_other6.03433.7082143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 83 -
Rwork0.351 1414 -
obs--96.15 %

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