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- PDB-4qeo: crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15... -

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Basic information

Entry
Database: PDB / ID: 4qeo
Titlecrystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
Components
  • DNA 5'-ACTGATGAGTACCAT-3'
  • DNA 5'-GGTACT(5CM)ATCAGTAT-3'
  • Histone H3
  • 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 / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / zinc ion binding / nucleoplasm / 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 / 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 / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Histone H3.2 / Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 / Histone H3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Synthetic construct (others)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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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'-GGTACT(5CM)ATCAGTAT-3'
D: DNA 5'-ACTGATGAGTACCAT-3'
P: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0909
Polymers70,4444
Non-polymers6465
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-15 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.460, 96.765, 122.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA 5'-GGTACT(5CM)ATCAGTAT-3'


Mass: 4598.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: DNA chain DNA 5'-ACTGATGAGTACCAT-3'


Mass: 4593.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Protein / Protein/peptide , 2 types, 2 molecules AP

#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
#4: Protein/peptide Histone H3


Mass: 1565.797 Da / Num. of mol.: 1 / Fragment: unp residues 2-16 / Source method: obtained synthetically
Details: H3(1-15) peptide was synthesized by Tufts University peptide facility.
Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133, UniProt: P84233*PLUS

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Non-polymers , 3 types, 290 molecules

#5: 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
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG200, 5% PEG3000, and 0.1 M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2013
RadiationMonochromator: double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 45325 / Num. obs: 45280 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 36.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4469 / Rsym value: 0.769 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4QEN

4qen


Resolution: 2→41.098 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 2271 5.02 %RANDOM
Rwork0.1864 ---
obs0.1883 45207 99.82 %-
all-45280 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→41.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 490 30 285 4570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114420
X-RAY DIFFRACTIONf_angle_d1.3676065
X-RAY DIFFRACTIONf_dihedral_angle_d20.9071682
X-RAY DIFFRACTIONf_chiral_restr0.092660
X-RAY DIFFRACTIONf_plane_restr0.008695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0004-2.04380.28561370.24472640X-RAY DIFFRACTION99
2.0438-2.09140.25171280.23262631X-RAY DIFFRACTION100
2.0914-2.14370.25881310.2262692X-RAY DIFFRACTION100
2.1437-2.20160.23481410.21552643X-RAY DIFFRACTION100
2.2016-2.26640.25121550.21332632X-RAY DIFFRACTION100
2.2664-2.33960.24341540.20732627X-RAY DIFFRACTION100
2.3396-2.42320.26011400.21022697X-RAY DIFFRACTION100
2.4232-2.52020.25241210.19722668X-RAY DIFFRACTION100
2.5202-2.63490.24641530.19612661X-RAY DIFFRACTION100
2.6349-2.77380.24561540.19662665X-RAY DIFFRACTION100
2.7738-2.94750.21911610.19572667X-RAY DIFFRACTION100
2.9475-3.1750.25081330.19852677X-RAY DIFFRACTION100
3.175-3.49440.22451270.18172729X-RAY DIFFRACTION100
3.4944-3.99960.18841360.16262733X-RAY DIFFRACTION100
3.9996-5.03770.18211540.15232734X-RAY DIFFRACTION100
5.0377-41.10630.24721460.19252840X-RAY DIFFRACTION98
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)
11.5926-0.24550.5770.9178-0.58143.4594-0.123-0.1525-0.01690.22630.03540.0619-0.1904-0.2550.06990.1760.02490.00720.15420.02160.1837-17.148819.706916.5122
20.3534-0.32080.12790.51280.10241.3837-0.08360.1484-0.18240.0474-0.0628-0.10190.33810.1439-0.02140.23090.01980.03860.22470.06130.2725-10.19149.57627.1217
30.9621-0.22580.10292.7049-1.74763.8275-0.004-0.01360.09220.0931-0.1893-0.3975-0.27050.23110.09720.3533-0.0657-0.00190.29310.12610.3639-2.91053.703445.1636
44.2223-0.1253-0.94643.6161-0.81210.5977-0.14480.21091.30490.2229-0.0309-1.2801-1.17021.4463-0.13160.9116-0.327-0.09661.15460.39471.321515.260517.507240.0777
52.8432-0.3770.30472.83571.0772.399-0.1268-0.5538-0.24130.54160.00330.8875-0.2518-0.90460.02550.3520.06850.1190.51140.01940.4255-31.489819.126618.4422
62.62430.26970.71742.01510.92070.8516-0.08340.1229-0.4519-0.1511-0.09741.12431.0323-1.0548-0.06740.5929-0.21960.04370.82680.11530.8107-34.62798.742221.8361
71.61160.5717-0.94281.55690.15171.0274-0.43460.83190.6528-0.1341-0.35130.352-1.1329-0.31410.92760.69620.2025-0.07870.73190.14460.6419-32.786630.576315.2873
80.03890.08590.16080.57170.7731.0819-0.5768-0.2625-0.27110.12690.2465-0.3622-0.5325-0.02640.17370.7381-0.05310.1870.93550.13370.98030.735216.392346.6034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 99 through 278 )
2X-RAY DIFFRACTION2chain 'A' and (resid 279 through 337 )
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 589 )
4X-RAY DIFFRACTION4chain 'A' and (resid 590 through 624 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 11 )
6X-RAY DIFFRACTION6chain 'D' and (resid 3 through 7 )
7X-RAY DIFFRACTION7chain 'D' and (resid 8 through 15 )
8X-RAY DIFFRACTION8chain 'P' and (resid 9 through 15 )

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