[English] 日本語
Yorodumi
- PDB-6u8w: Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u8w
TitleCrystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA
Components
  • (DNA (cytosine-5)-methyltransferase ...) x 2
  • CpGpT DNA (25-MER)
KeywordsTransferase/DNA / DNMT3B / DNMT3L / DNA methylation / Methyltransferase / transferase-DNA complex / TRANSFERASE
Function / homology
Function and homology information


epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates ...epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity / genomic imprinting / 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 / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression, epigenetic / male meiosis I / catalytic complex / heterochromatin / enzyme activator activity / DNA methylation / condensed nuclear chromosome / PRC2 methylates histones and DNA / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / stem cell differentiation / placenta development / NoRC negatively regulates rRNA expression / transcription corepressor activity / spermatogenesis / methylation / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3B, ADD domain / 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. ...DNA (cytosine-5)-methyltransferase 3B, ADD domain / 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 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Vaccinia Virus protein VP39 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (cytosine-5)-methyltransferase 3B / DNA (cytosine-5)-methyltransferase 3-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94891558608 Å
AuthorsGao, L. / Zhang, Z.M. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2020
Title: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms.
Authors: Gao, L. / Emperle, M. / Guo, Y. / Grimm, S.A. / Ren, W. / Adam, S. / Uryu, H. / Zhang, Z.M. / Chen, D. / Yin, J. / Dukatz, M. / Anteneh, H. / Jurkowska, R.Z. / Lu, J. / Wang, Y. / ...Authors: Gao, L. / Emperle, M. / Guo, Y. / Grimm, S.A. / Ren, W. / Adam, S. / Uryu, H. / Zhang, Z.M. / Chen, D. / Yin, J. / Dukatz, M. / Anteneh, H. / Jurkowska, R.Z. / Lu, J. / Wang, Y. / Bashtrykov, P. / Wade, P.A. / Wang, G.G. / Jeltsch, A. / Song, J.
History
DepositionSep 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 3B
B: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3B
E: CpGpT DNA (25-MER)
F: CpGpT DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,79910
Polymers129,9826
Non-polymers8174
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.506, 193.506, 49.869
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31

-
Components

-
DNA (cytosine-5)-methyltransferase ... , 2 types, 4 molecules ADBC

#1: Protein DNA (cytosine-5)-methyltransferase 3B / Dnmt3b / DNA methyltransferase HsaIIIB / M.HsaIIIB


Mass: 33128.312 Da / Num. of mol.: 2 / Mutation: K777A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli) / Variant (production host): DE3
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 24163.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Production host: Escherichia coli (E. coli) / Variant (production host): DE3 / References: UniProt: Q9UJW3

-
DNA chain , 1 types, 2 molecules EF

#3: DNA chain CpGpT DNA (25-MER)


Mass: 7698.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 3 types, 15 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.29 Å3/Da / Density % sol: 71.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.94891558608→48.38 Å / Num. obs: 43944 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 76.8711214453 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.91
Reflection shellResolution: 2.95→3.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 4333 / CC1/2: 0.782

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YX2

5yx2


Resolution: 2.94891558608→48.3765 Å / SU ML: 0.458235129573 / Cross valid method: FREE R-VALUE / σ(F): 1.96341412436 / Phase error: 27.4313585176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236316819954 1977 4.50783227307 %
Rwork0.215787357675 41880 -
obs0.216714672433 43857 99.6500874781 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.2882784718 Å2
Refinement stepCycle: LAST / Resolution: 2.94891558608→48.3765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7324 1020 54 11 8409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003567402804228752
X-RAY DIFFRACTIONf_angle_d0.68541036679112130
X-RAY DIFFRACTIONf_chiral_restr0.04231267462981325
X-RAY DIFFRACTIONf_plane_restr0.004776528082521393
X-RAY DIFFRACTIONf_dihedral_angle_d24.23494479843175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94891558608-3.02260.4399747057911420.3911535008742984X-RAY DIFFRACTION98.8302244704
3.0226-3.10440.3617157761081380.3156227218842967X-RAY DIFFRACTION99.36
3.1044-3.19570.3145492611991420.2959209495552976X-RAY DIFFRACTION99.5530012771
3.1957-3.29880.3268741623971400.2869722157073010X-RAY DIFFRACTION99.652008858
3.2988-3.41670.2815350260421340.2660879951082930X-RAY DIFFRACTION99.5775105622
3.4167-3.55350.3147372838691480.2648091431683047X-RAY DIFFRACTION99.8749609253
3.5535-3.71510.228161539291400.2403046015982994X-RAY DIFFRACTION99.9043672298
3.7151-3.91090.2234192723491340.2140174153022997X-RAY DIFFRACTION99.8724082935
3.9109-4.15580.2212024954551520.2091729575183014X-RAY DIFFRACTION99.8738170347
4.1558-4.47650.1900490861331400.173814112452981X-RAY DIFFRACTION99.6169805298
4.4765-4.92660.182591369341460.1841906625113001X-RAY DIFFRACTION100
4.9266-5.63850.2289129325081460.187297471322985X-RAY DIFFRACTION99.8405612245
5.6385-7.10030.2110272163431330.2080294741813019X-RAY DIFFRACTION99.9365884591
7.1003-48.37650.2274248836981420.1849810992212975X-RAY DIFFRACTION99.3307839388

+
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