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- PDB-4qep: crystal structure of KRYPTONITE in complex with mCHG DNA and SAH -

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Basic information

Entry
Database: PDB / ID: 4qep
Titlecrystal structure of KRYPTONITE in complex with mCHG DNA and SAH
Components
  • DNA (5'-D(*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3')
  • DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*TP*AP*T)-3')
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
Keywordstranscription/DNA / SRA / SET / Histone methylation / methylated DNA / Methylation / transcription-DNA complex
Function / homology
Function and homology information


methyl-CpNpG binding / methyl-CpNpN binding / peptidyl-lysine methylation / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / double-stranded methylated DNA binding / methyl-CpG binding / chromosome, centromeric region / Transferases; Transferring one-carbon groups; Methyltransferases ...methyl-CpNpG binding / methyl-CpNpN binding / peptidyl-lysine methylation / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / double-stranded methylated DNA binding / methyl-CpG binding / chromosome, centromeric region / Transferases; Transferring one-carbon groups; Methyltransferases / zinc ion binding / nucleus
Similarity search - Function
Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. ...Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / Post-SET domain / Post-SET domain profile. / PUA-like superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDu, J. / Li, S. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2014
Title: Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE.
Authors: Du, J. / Johnson, L.M. / Groth, M. / Feng, S. / Hale, C.J. / Li, S. / Vashisht, A.A. / Gallego-Bartolome, J. / Wohlschlegel, J.A. / Patel, D.J. / Jacobsen, S.E.
History
DepositionMay 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
C: DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*TP*AP*T)-3')
D: DNA (5'-D(*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5258
Polymers68,8793
Non-polymers6465
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-15 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.346, 95.569, 121.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the asymmetric unit.

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 / Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 / Protein KRYPTONITE / Protein SET DOMAIN GROUP ...Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 / Protein KRYPTONITE / Protein SET DOMAIN GROUP 33 / Suppressor of variegation 3-9 homolog protein 4 / Su(var)3-9 homolog protein 4


Mass: 59686.797 Da / Num. of mol.: 1 / Fragment: functional fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUVH4, KYP, SDG33, SET33, At5g13960, MAC12.7 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q8GZB6, histone-lysine N-methyltransferase
#2: DNA chain DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*TP*AP*T)-3')


Mass: 4623.037 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3')


Mass: 4568.985 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG200, 5% PEG3000, and 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2013
RadiationMonochromator: double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 12077 / Num. obs: 10851 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.155 / Rsym value: 0.155 / Net I/σ(I): 9.5
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2 / Rsym value: 0.615 / % possible all: 92.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4QEN

4qen


Resolution: 3.1→49.627 Å / SU ML: 0.44 / σ(F): 1.37 / Phase error: 27.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.251 516 4.77 %RANDOM
Rwork0.2102 ---
obs0.2122 10811 89.76 %-
all-12044 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→49.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3690 490 30 0 4210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164344
X-RAY DIFFRACTIONf_angle_d1.6015964
X-RAY DIFFRACTIONf_dihedral_angle_d22.0921653
X-RAY DIFFRACTIONf_chiral_restr0.091650
X-RAY DIFFRACTIONf_plane_restr0.007681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.41190.34641350.25562588X-RAY DIFFRACTION92
3.4119-3.90550.24411430.20472585X-RAY DIFFRACTION92
3.9055-4.91980.19641180.18012564X-RAY DIFFRACTION90
4.9198-49.6330.25991200.21922558X-RAY DIFFRACTION85
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)
11.86720.53610.69810.94190.63923.4195-0.04490.141-0.0752-0.14250.0426-0.0105-0.0783-0.0570.00220.2097-0.02640.00090.2108-0.02250.2033-9.286319.1529-14.485
21.28330.20240.90341.71821.60662.8504-0.0309-0.0068-0.0331-0.077-0.16630.2170.1199-0.26270.12560.21980.02090.02070.22630.0030.325-24.54794.056-43.6655
31.5390.05160.20542.0497-0.17281.8662-0.1382-0.17790.61320.0203-0.10240.6473-0.3073-0.78490.12450.32550.1288-0.020.4439-0.17260.5255-32.460514.9148-42.3902
46.40531.82791.24285.9688-0.64265.0301-0.07551.0331-0.3338-0.44520.4045-1.1458-0.0463-0.0504-0.25690.37730.07090.14310.438-0.180.30694.549818.357-18.4039
54.2947-0.52830.46493.5766-4.2024.9483-0.12710.0896-0.215-0.2895-0.3269-0.53470.7010.7020.29820.49590.31580.03130.63580.0530.42617.70647.4389-20.8996
64.4582-1.6502-0.1233.3312-0.10222.0085-0.7376-0.23740.3302-0.1373-0.0657-0.8008-0.6480.16720.3810.6164-0.1512-0.12760.35390.07510.37316.34630.132-15.5234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 99 through 302 )
2X-RAY DIFFRACTION2chain 'A' and (resid 303 through 564 )
3X-RAY DIFFRACTION3chain 'A' and (resid 565 through 624 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 11 )
5X-RAY DIFFRACTION5chain 'D' and (resid 3 through 7 )
6X-RAY DIFFRACTION6chain 'D' and (resid 8 through 15 )

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