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- PDB-5hq2: Structural model of Set8 histone H4 Lys20 methyltransferase bound... -

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Basic information

Entry
Database: PDB / ID: 5hq2
TitleStructural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle
Components
  • (DNA (149-MER)) x 2
  • Guanine nucleotide exchange factor SRM1
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • N-lysine methyltransferase SETD8
KeywordsTransferase/DNA / chromatin enzyme / chromatin complex / epigenetics / histone methyltransferase / Transferase-DNA complex
Function / homology
Function and homology information


response to pheromone / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / polytene chromosome / peptidyl-lysine monomethylation / Postmitotic nuclear pore complex (NPC) reformation / mitotic chromosome condensation ...response to pheromone / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / polytene chromosome / peptidyl-lysine monomethylation / Postmitotic nuclear pore complex (NPC) reformation / mitotic chromosome condensation / protein-lysine N-methyltransferase activity / regulation of mitotic spindle assembly / regulation of DNA damage response, signal transduction by p53 class mediator / poly(A)+ mRNA export from nucleus / histone methyltransferase activity / nucleus organization / negative regulation of double-strand break repair via homologous recombination / ribosomal subunit export from nucleus / regulation of mitotic cell cycle / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / guanyl-nucleotide exchange factor activity / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / protein import into nucleus / transcription corepressor activity / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 1. / Class V SAM-dependent methyltransferases / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / : / : / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 ...Regulator of chromosome condensation (RCC1) signature 1. / Class V SAM-dependent methyltransferases / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / : / : / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Guanine nucleotide exchange factor SRM1 / Histone H4 / Histone H3.2 / Histone H2A / N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
Saccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsTavarekere, G. / McGinty, R.K. / Tan, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088236 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111651 United States
Damon Runyon Cancer Research FoundationDRG 2107-12 United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate.
Authors: Girish, T.S. / McGinty, R.K. / Tan, S.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 H3.2
B: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (149-MER)
J: DNA (149-MER)
K: Guanine nucleotide exchange factor SRM1
M: N-lysine methyltransferase SETD8


Theoretical massNumber of molelcules
Total (without water)222,1678
Polymers222,1678
Non-polymers00
Water00
1
A: Histone H3.2
B: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (149-MER)
J: DNA (149-MER)
K: Guanine nucleotide exchange factor SRM1
M: N-lysine methyltransferase SETD8

A: Histone H3.2
B: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (149-MER)
J: DNA (149-MER)
K: Guanine nucleotide exchange factor SRM1
M: N-lysine methyltransferase SETD8


Theoretical massNumber of molelcules
Total (without water)444,33316
Polymers444,33316
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)100.729, 300.752, 182.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsGel filtration used to confirm assembly

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Components

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Protein , 6 types, 6 molecules ABGHKM

#1: Protein Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281
#7: Protein Guanine nucleotide exchange factor SRM1 / Pheromone response pathway component SRM1 / Pre-mRNA-processing protein 20 / Regulator of ...Pheromone response pathway component SRM1 / Pre-mRNA-processing protein 20 / Regulator of chromosome condensation / Suppressor of receptor mutations 1 / mRNA transport protein 1


Mass: 53095.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SRM1, MTR1, PRP20, YGL097W / Plasmid: pST50Tr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P21827
#8: Protein N-lysine methyltransferase SETD8 / H4-K20-HMTase SETD8 / Histone-lysine N-methyltransferase SETD8 / Lysine N-methyltransferase 5A / ...H4-K20-HMTase SETD8 / Histone-lysine N-methyltransferase SETD8 / Lysine N-methyltransferase 5A / PR/SET domain-containing protein 07 / PR/SET07 / SET domain-containing protein 8


Mass: 23016.270 Da / Num. of mol.: 1 / Mutation: H347F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD8, KMT5A, PRSET7, SET07, SET8 / Plasmid: pST50Tr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS
References: UniProt: Q9NQR1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (149-MER)


Mass: 45772.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: WIDOM 601 nucleosome positioning sequence / Plasmid: plasmid / Details (production host): PST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
#6: DNA chain DNA (149-MER)


Mass: 46212.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: WIDOM 601 nucleosome positioning sequence / Plasmid: plasmid / Details (production host): PST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5.5
Details: 25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME
PH range: 5.5-6

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid N2 stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.5→46.19 Å / Num. all: 16854 / Num. obs: 16854 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.9
Reflection shellResolution: 4.5→4.74 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→46 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.832 / SU B: 124.392 / SU ML: 1.58 / Cross valid method: THROUGHOUT / ESU R Free: 1.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3972 845 5 %RANDOM
Rwork0.33904 ---
obs0.34184 15908 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 171.987 Å2
Baniso -1Baniso -2Baniso -3
1-11.93 Å20 Å2-0 Å2
2---7.31 Å20 Å2
3----4.62 Å2
Refinement stepCycle: LAST / Resolution: 4.5→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 2971 0 0 7738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0168112
X-RAY DIFFRACTIONr_bond_other_d0.0040.024618
X-RAY DIFFRACTIONr_angle_refined_deg0.991.61611783
X-RAY DIFFRACTIONr_angle_other_deg1.359310286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.21316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028379
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021646
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_it9.96721.7973827
X-RAY DIFFRACTIONr_mcbond_other9.95121.7963826
X-RAY DIFFRACTIONr_mcangle_it17.74332.6584768
X-RAY DIFFRACTIONr_mcangle_other17.74332.664769
X-RAY DIFFRACTIONr_scbond_it10.88622.7294285
X-RAY DIFFRACTIONr_scbond_other10.88522.7314286
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.72734.0127015
X-RAY DIFFRACTIONr_long_range_B_refined27.0759255
X-RAY DIFFRACTIONr_long_range_B_other27.0769256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.5→4.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 55 -
Rwork0.36 1125 -
obs--96.48 %

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