[English] 日本語
Yorodumi
- PDB-4qep: crystal structure of KRYPTONITE in complex with mCHG DNA and SAH -

+
Open data


ID or keywords:

Loading...

-
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 / double-stranded methylated DNA binding / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / 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 / double-stranded methylated DNA binding / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / 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 motif / Pre-SET domain ...: / 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 motif / Pre-SET domain / 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 / SET domain profile. / SET domain superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more