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- PDB-5wbv: Crystal Structure of the SET Domain of Human SUV420H1 In Complex ... -

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Basic information

Entry
Database: PDB / ID: 5wbv
TitleCrystal Structure of the SET Domain of Human SUV420H1 In Complex With Inhibitor
ComponentsHistone-lysine N-methyltransferase KMT5B
KeywordsTRANSFERASE/INHIBITOR / SET domain / methyltransferase / protein-inhibitor complex / SGC / Structural Genomics / Structural Genomics Consortium / TRANSFERASE / 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
Histone-lysine N-methyltransferase / 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. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain ...Histone-lysine N-methyltransferase / 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. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Beta Complex / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-9ZY / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase KMT5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsHalabelian, L. / Tempel, W. / Brown, P.J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal Structure of the SET Domain of Human SUV420H1 In Complex With Inhibitor
Authors: Halabelian, L. / Tempel, W. / Brown, P.J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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: Histone-lysine N-methyltransferase KMT5B
B: Histone-lysine N-methyltransferase KMT5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,88920
Polymers63,2002
Non-polymers1,68918
Water55831
1
A: Histone-lysine N-methyltransferase KMT5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,44410
Polymers31,6001
Non-polymers8459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase KMT5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,44410
Polymers31,6001
Non-polymers8459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.324, 50.559, 74.818
Angle α, β, γ (deg.)101.260, 107.510, 89.670
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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 / Suv4-20h1


Mass: 31599.756 Da / Num. of mol.: 2 / Fragment: SET domain, UNP residues 63-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT5B, SUV420H1, CGI-85 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V3R-pRARE2
References: UniProt: Q4FZB7, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 49 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-9ZY / 2-chloro-5-(4-methyl-6-oxo-3-phenylpyrano[2,3-c]pyrazol-1(6H)-yl)benzoic acid


Mass: 380.781 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H13ClN2O4
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.49 % / Mosaicity: 0.34 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8-12% EtOH, 100mM Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→37.01 Å / Num. obs: 26973 / % possible obs: 95.8 % / Redundancy: 2.2 % / Biso Wilson estimate: 53.33 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.05 / Rrim(I) all: 0.073 / Net I/σ(I): 10.7 / Num. measured all: 59075 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.382.20.435559225520.7460.3950.5892.293
8.91-37.012.10.03510214770.990.0330.04824.897.9

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3S8P

3s8p


Resolution: 2.3→37 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.867 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.271 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1351 5.01 %RANDOM
Rwork0.234 ---
obs0.236 26949 95.7 %-
Displacement parametersBiso max: 145.32 Å2 / Biso mean: 53.74 Å2 / Biso min: 27.81 Å2
Baniso -1Baniso -2Baniso -3
1-12.763 Å2-3.9535 Å23.2026 Å2
2---4.3488 Å2-1.1017 Å2
3----8.4142 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.3→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 122 31 3549
Biso mean--44.04 42.96 -
Num. residues----460
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1207SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes627HARMONIC5
X-RAY DIFFRACTIONt_it3618HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion481SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4028SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3618HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4913HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion18.28
LS refinement shellResolution: 2.3→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.29 130 4.78 %
Rwork0.249 2587 -
all0.251 2717 -
obs--92.94 %
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)
12.26270.18390.51182.614-0.96632.2532-0.0337-0.24050.00260.1346-0.0174-0.1058-0.03690.1160.0511-0.1885-0.00310.0733-0.1695-0.0469-0.05516.128844.16147.5616
21.9964-0.25890.48563.8531.91283.0571-0.06330.2578-0.0970.0004-0.17310.3387-0.0356-0.10620.2364-0.2482-0.03480.0943-0.1871-0.1141-0.08424.299618.4688-18.0052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A72 - 333
2X-RAY DIFFRACTION2{ B|* }B71 - 333

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