[English] 日本語
Yorodumi
- PDB-1khc: Crystal Structure of the PWWP Domain of Mammalian DNA Methyltrans... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1khc
TitleCrystal Structure of the PWWP Domain of Mammalian DNA Methyltransferase Dnmt3b
ComponentsDNA cytosine-5 methyltransferase 3B2
KeywordsTRANSFERASE / Five beta-sheets barrel followed by Five-helix bundle
Function / homology
Function and homology information


gene silencing by piRNA-directed DNA methylation / SUMOylation of DNA methylation proteins / epigenetic programming of gene expression / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / transposable element silencing by heterochromatin formation / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase ...gene silencing by piRNA-directed DNA methylation / SUMOylation of DNA methylation proteins / epigenetic programming of gene expression / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / transposable element silencing by heterochromatin formation / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / autosome genomic imprinting / protein-containing complex localization / DNA methylation-dependent constitutive heterochromatin formation / lncRNA binding / negative regulation of gene expression, epigenetic / chromosome, centromeric region / heterochromatin / epigenetic regulation of gene expression / methyltransferase activity / cellular response to amino acid stimulus / heterochromatin formation / methylation / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site ...PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsQiu, C. / Sawada, K. / Zhang, X. / Cheng, X.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.
Authors: Qiu, C. / Sawada, K. / Zhang, X. / Cheng, X.
History
DepositionNov 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE AUTHORS WERE UNABLE TO FIGURE OUT THE IDENTITY OF THE MOLECULES LABELED AS "UNX" FROM ...HETEROGEN THE AUTHORS WERE UNABLE TO FIGURE OUT THE IDENTITY OF THE MOLECULES LABELED AS "UNX" FROM THE ELECTRON DENSITY.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA cytosine-5 methyltransferase 3B2


Theoretical massNumber of molelcules
Total (without water)16,67023
Polymers16,6701
Non-polymers022
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.750, 52.750, 186.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-49-

HOH

21A-140-

HOH

31A-150-

HOH

-
Components

#1: Protein DNA cytosine-5 methyltransferase 3B2


Mass: 16670.039 Da / Num. of mol.: 1 / Fragment: PWWP domain (residues 219-365)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt3b / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O88509, DNA (cytosine-5-)-methyltransferase
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 22 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 8000, 0.1M sodium cacodylate, 0.2M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
124 mg/mlprotein1drop
220 mMHEPES1droppH7.0
3200 mM1dropNaCl
41 mMEDTA1drop
55 %(v/v)glycerol1drop
630 %(w/v)PEG80001reservoir
7200 mMsodium acetate1reservoir
8100 mMsodium cacodylate1reservoirpH6.5

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 27, 2000
RadiationMonochromator: confocal multilayer mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 15308 / Num. obs: 15308 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 9.4 / % possible all: 94.3
Reflection
*PLUS
Num. measured all: 145433
Reflection shell
*PLUS
% possible obs: 94.3 %

-
Processing

Software
NameClassification
SOLVEphasing
RESOLVEmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1477 10 %random
Rwork0.19 ---
obs-14656 97.1 %-
Displacement parametersBiso mean: 15.442 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 22 162 1241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d24.219
X-RAY DIFFRACTIONx_improper_angle_d0.615
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.282 166 11.4 %
Rwork0.275 1450 -
obs--87.7 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.219
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.615
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.282 / % reflection Rfree: 11.4 % / Rfactor Rwork: 0.275

+
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