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- PDB-4qen: crystal structure of KRYPTONITE in complex with mCHH DNA and SAH -

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Basic information

Entry
Database: PDB / ID: 4qen
Titlecrystal structure of KRYPTONITE in complex with mCHH DNA and SAH
Components
  • DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3')
  • DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*TP*CP*AP*GP*TP*AP*T)-3')
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4Histone methyltransferase
Keywordstranscription/DNA / SRA / SET / histone methylation / methylated DNA / 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 ...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 / SAD / Resolution: 2.002 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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*TP*CP*AP*GP*TP*AP*T)-3')
D: DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5248
Polymers68,8783
Non-polymers6465
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-18 kcal/mol
Surface area25410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.395, 98.009, 122.581
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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Protein , 1 types, 1 molecules A

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 / Histone methyltransferase / 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

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*TP*CP*AP*GP*TP*AP*T)-3')


Mass: 4598.023 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3')


Mass: 4593.010 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 388 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
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: NSLS / Beamline: X29A / Wavelength: 1.283 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: 1.283 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 44995 / Num. obs: 44950 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 48.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4416 / Rsym value: 0.61 / % 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: SAD / Resolution: 2.002→40.683 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 2261 5.04 %RANDOM
Rwork0.176 ---
obs0.1777 44884 99.91 %-
all-44924 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→40.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 490 30 383 4624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084377
X-RAY DIFFRACTIONf_angle_d1.416011
X-RAY DIFFRACTIONf_dihedral_angle_d18.2681666
X-RAY DIFFRACTIONf_chiral_restr0.099654
X-RAY DIFFRACTIONf_plane_restr0.005689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0021-2.02480.25711360.24582633X-RAY DIFFRACTION99
2.0248-2.04860.27821540.23432687X-RAY DIFFRACTION100
2.0486-2.07360.24081310.21822756X-RAY DIFFRACTION100
2.0736-2.09990.28351900.21612651X-RAY DIFFRACTION100
2.0999-2.12750.26691460.20582661X-RAY DIFFRACTION100
2.1275-2.15660.22581340.1912743X-RAY DIFFRACTION100
2.1566-2.18740.26391360.18872706X-RAY DIFFRACTION100
2.1874-2.22010.20591200.19012688X-RAY DIFFRACTION100
2.2201-2.25480.26911250.19122691X-RAY DIFFRACTION100
2.2548-2.29170.22331670.18532701X-RAY DIFFRACTION100
2.2917-2.33130.25861290.18272703X-RAY DIFFRACTION100
2.3313-2.37360.20231560.18662721X-RAY DIFFRACTION100
2.3736-2.41930.21151510.18432626X-RAY DIFFRACTION100
2.4193-2.46870.22741310.18042735X-RAY DIFFRACTION100
2.4687-2.52230.23051720.17972681X-RAY DIFFRACTION100
2.5223-2.5810.22461390.18072738X-RAY DIFFRACTION100
2.581-2.64550.24481300.18582669X-RAY DIFFRACTION100
2.6455-2.71710.25011480.18322735X-RAY DIFFRACTION100
2.7171-2.7970.17071260.18572715X-RAY DIFFRACTION100
2.797-2.88720.24221410.18362691X-RAY DIFFRACTION100
2.8872-2.99040.22461470.18432694X-RAY DIFFRACTION100
2.9904-3.11010.21381640.17762656X-RAY DIFFRACTION100
3.1101-3.25160.20871480.17932710X-RAY DIFFRACTION100
3.2516-3.42290.21111260.16532727X-RAY DIFFRACTION100
3.4229-3.63730.17941360.16432719X-RAY DIFFRACTION100
3.6373-3.91790.19021570.15842680X-RAY DIFFRACTION100
3.9179-4.31180.17611360.14792689X-RAY DIFFRACTION100
4.3118-4.93480.17641390.14242683X-RAY DIFFRACTION100
4.9348-6.21370.20051480.17132693X-RAY DIFFRACTION100
6.2137-40.69190.22021250.20192691X-RAY DIFFRACTION99
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)
11.2101-0.20560.54731.2382-1.12053.276-0.1616-0.26550.07960.14650.12780.0113-0.3502-0.16470.120.26120.0486-0.03130.2665-0.00140.1976-16.368122.036525.1445
21.6513-0.34810.48831.4138-0.24242.7042-0.03560.0256-0.0740.04340.00910.08450.0818-0.0809-0.0130.2182-0.00630.01090.16580.00160.1885-18.987817.15076.2399
30.1182-0.29720.56441.539-1.34752.1880.06990.1764-0.0702-0.5023-0.2533-0.32390.87140.57040.16370.42730.10080.04830.43580.06630.40035.6574-2.415730.8512
41.3855-0.47190.14172.0041-1.10812.671-0.04050.05490.16390.1602-0.0662-0.2918-0.17490.13120.09660.222-0.0103-0.04670.1950.05950.275-2.14087.879746.1133
53.5866-0.77740.17282.36070.26864.23150.0282-0.7427-0.39190.20140.16010.70680.0897-0.7429-0.25660.2756-0.02320.02440.38870.04580.3344-31.550118.32618.3796
63.907-3.8835-0.97376.7484-1.41792.6129-0.24830.352-1.1088-0.4905-0.23280.76230.8544-1.0813-0.21260.4526-0.17590.04380.6825-0.01810.6117-34.58788.011521.1245
70.71580.9028-0.71641.9118-0.0641.7759-0.44530.10050.3290.23010.19720.6676-0.8043-0.7334-0.02480.45720.1479-0.1110.48810.03740.4222-33.356130.367915.8184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 99 through 186 )
2X-RAY DIFFRACTION2chain 'A' and (resid 187 through 302 )
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 368 )
4X-RAY DIFFRACTION4chain 'A' and (resid 369 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 )

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