[English] 日本語
Yorodumi
- PDB-6kda: Crystal structure of human DNMT3B-DNMT3L in complex with DNA cont... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kda
TitleCrystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpG site
Components
  • DNA (25-MER)
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3B
KeywordsTRANSFERASE/DNA / DNMT3B / DNA methyltransferase / complex / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


epigenetic programing of female pronucleus / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / DNA-methyltransferase activity / transposable element silencing by heterochromatin formation / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting ...epigenetic programing of female pronucleus / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / DNA-methyltransferase activity / transposable element silencing by heterochromatin formation / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / genomic imprinting / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / male meiosis I / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / catalytic complex / heterochromatin / DNA methylation / placenta development / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / stem cell differentiation / enzyme activator activity / NoRC negatively regulates rRNA expression / transcription corepressor activity / spermatogenesis / methylation / negative regulation of DNA-templated transcription / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.909 Å
AuthorsLin, C.-C. / Chen, Y.-P. / Yang, W.-Z. / Shen, C.-K. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.
Authors: Lin, C.C. / Chen, Y.P. / Yang, W.Z. / Shen, J.C.K. / Yuan, H.S.
History
DepositionJul 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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

-
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: DNA (25-MER)
F: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8478
Polymers128,0786
Non-polymers7692
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12600 Å2
ΔGint-59 kcal/mol
Surface area48170 Å2
Unit cell
Length a, b, c (Å)193.872, 193.872, 49.741
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

-
Components

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


Mass: 32715.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 23627.107 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) / References: UniProt: Q9UJW3
#3: DNA chain DNA (25-MER)


Mass: 7696.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.29 Å3/Da / Density % sol: 71.36 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0 mM MES (pH 5.7), 160 mM KCl, 10 mM MgSO4 and 14% PEG 400

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.909→30 Å / Num. obs: 42182 / % possible obs: 100 % / Redundancy: 4.8 % / CC1/2: 0.972 / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.95
Reflection shellResolution: 2.91→3.01 Å / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 2208 / CC1/2: 0.852 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YX2

5yx2


Resolution: 2.909→29.5 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.99
RfactorNum. reflection% reflection
Rfree0.2199 2100 4.98 %
Rwork0.1876 --
obs0.1892 42169 91.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 245.46 Å2 / Biso min: 8.51 Å2
Refinement stepCycle: final / Resolution: 2.909→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7625 1022 52 305 9004
Biso mean--26.6 43.38 -
Num. residues----989
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9094-2.9770.320885130346
2.977-3.05140.260280168058
3.0514-3.13380.2257118226878
3.1338-3.22590.2566177287799
3.2259-3.32990.25081532877100
3.3299-3.44870.29131142937100
3.4487-3.58660.27822002891100
3.5866-3.74950.22721912847100
3.7495-3.94670.24821572900100
3.9467-4.19340.21081150.16622949100
4.1934-4.51610.19411780.14992899100
4.5161-4.96860.19831520.15512899100
4.9686-5.68310.18651042943100
5.6831-7.14330.20241442928100
7.14330.16891320.185287199
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)
15.76240.76480.33273.0167-0.38664.06250.0760.1264-0.3174-0.0609-0.11710.55760.3107-0.42160.05620.3619-0.1877-0.08520.2962-0.05620.345313.7513-79.0635-10.4383
23.86091.35411.47132.39410.43882.89760.3078-0.6466-0.39610.6797-0.21860.3475-0.03660.0845-0.11130.4828-0.19010.01790.51480.05260.094527.0664-72.41353.6671
33.89181.48484.50758.03584.75056.45750.1247-0.04930.2429-0.01670.08690.95460.2626-0.9728-0.14390.5025-0.2811-0.18291.1437-0.25551.7407-22.4276-88.0278-20.3169
49.43851.49272.47774.4461-0.81356.3082-0.1648-0.15650.84830.0891-0.21341.0164-0.1659-0.73940.33470.3395-0.1028-0.07210.7157-0.26491.1011-9.9808-78.9592-13.1398
54.4084-5.14414.23546.0894-4.71914.4951-0.5085-0.06561.39380.04470.45440.7989-0.7791-0.92440.09330.74590.0075-0.48831.15520.05181.8924-14.3754-68.087-26.5519
69.3108-4.5605-0.25093.6946-0.08784.9498-0.03991.28852.0097-0.9442-0.28850.7303-0.6971-0.85270.37210.6825-0.0575-0.58441.09370.16151.6306-13.6577-70.9194-26.3994
74.85691.403-1.66324.42160.32083.9277-0.08190.29090.6244-0.0891-0.29961.5564-0.7008-0.66360.36851.02360.073-0.46131.1773-0.03212.6048-16.3863-58.2897-19.6318
86.20843.96491.93635.11081.02092.9997-0.12190.32171.1172-0.29570.09541.3711-0.0396-0.9380.13550.7611-0.1993-0.47911.2795-0.12541.8061-24.2806-82.6689-25.9339
94.08481.02911.56750.89751.33532.86930.1596-0.51870.6380.09870.18090.0238-0.57690.4216-0.25740.7129-0.4686-0.43640.95390.02531.681186.657-25.26319.6124
107.1342.01720.10744.6743-1.0580.29030.14890.2131.3399-0.52650.1374-0.8101-1.20011.375-0.30831.2366-0.614-0.35461.30210.0992.071691.7478-19.63732.5317
115.65664.00290.30256.39283.05025.6738-0.51630.78720.6187-0.83490.4752-0.4924-0.75590.8885-0.0810.538-0.3163-0.24310.73370.09591.293981.0007-31.2816-3.589
121.0637-0.7401-0.18094.18821.13620.307-0.18950.95922.6718-1.7454-0.34141.5577-2.3049-1.07750.53851.28220.0349-0.60390.93070.29582.235564.177-20.3833-4.1353
135.23714.99180.07696.19013.1766.7786-0.1837-0.08860.84120.2064-0.14160.1144-0.1930.22040.25940.507-0.2038-0.23610.4970.00791.089473.8913-32.67133.9284
140.13820.06-0.81492.00474.62937.15710.0226-0.45111.97790.4764-0.40271.2212-0.7345-0.85430.40530.7153-0.1297-0.21970.7836-0.31451.611963.5847-27.927710.9335
151.0425-0.9296-0.48332.00391.80061.14280.0102-0.92641.09991.1318-0.43251.8041-0.6087-0.48040.47021.1101-0.247-0.15080.9089-0.52981.74668.5307-23.301315.1649
164.52546.0519-5.21428.9903-5.20769.4002-0.096-0.18730.436-0.07090.25410.3679-0.309-0.863-0.09981.1378-0.0986-0.04661.0235-0.70872.792655.9947-15.43239.6295
177.085-0.5120.53132.72040.99283.64390.4762-0.31370.52270.2517-0.41790.9881-0.78090.26690.06151.0127-0.3499-0.3481.0176-0.35431.749283.743-20.29213.9684
184.35361.60390.00454.30820.3644.3615-0.0494-0.00670.31220.2463-0.0155-0.5989-0.21090.39350.06420.1473-0.0696-0.07110.4873-0.05390.350461.5693-51.4408-1.6961
193.36471.37930.8082.72411.07362.7469-0.14540.9440.1667-0.38410.1771-0.6405-0.033-0.0469-0.06860.3317-0.12310.05030.6621-0.01330.045449.1917-59.6406-15.8285
205.4605-1.56442.77318.0254.18864.6769-0.04020.68631.4821-0.8620.29991.96580.3825-1.3723-0.28161.2167-0.01050.21321.50060.72181.792439.4004-41.9006-17.2782
218.95016.8862-5.15145.8503-5.266.0781.2837-0.55283.58271.4606-0.61742.1636-2.46312.2734-0.64341.7878-0.59230.16441.56590.05952.153711.7898-57.44688.194
229.3729-1.49972.725.3899-1.06245.2220.5153-1.31962.93121.0787-0.67110.349-1.29841.23220.09621.492-0.20080.49611.2316-0.18391.638116.5459-55.07415.1491
239.9389-3.6202-5.15342.019-1.9672.01880.14142.22133.8546-0.17470.62311.99110.5478-2.8768-0.78521.1889-0.11210.05841.95840.08192.15443.8414-38.9136-20.4091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 570 through 725 )A570 - 725
2X-RAY DIFFRACTION2chain 'A' and (resid 726 through 853 )A726 - 853
3X-RAY DIFFRACTION3chain 'B' and (resid 176 through 217 )B176 - 217
4X-RAY DIFFRACTION4chain 'B' and (resid 218 through 301 )B218 - 301
5X-RAY DIFFRACTION5chain 'B' and (resid 302 through 318 )B302 - 318
6X-RAY DIFFRACTION6chain 'B' and (resid 319 through 339 )B319 - 339
7X-RAY DIFFRACTION7chain 'B' and (resid 340 through 360 )B340 - 360
8X-RAY DIFFRACTION8chain 'B' and (resid 361 through 379 )B361 - 379
9X-RAY DIFFRACTION9chain 'C' and (resid 178 through 206 )C178 - 206
10X-RAY DIFFRACTION10chain 'C' and (resid 207 through 217 )C207 - 217
11X-RAY DIFFRACTION11chain 'C' and (resid 218 through 244 )C218 - 244
12X-RAY DIFFRACTION12chain 'C' and (resid 245 through 255 )C245 - 255
13X-RAY DIFFRACTION13chain 'C' and (resid 256 through 291 )C256 - 291
14X-RAY DIFFRACTION14chain 'C' and (resid 292 through 318 )C292 - 318
15X-RAY DIFFRACTION15chain 'C' and (resid 319 through 339 )C319 - 339
16X-RAY DIFFRACTION16chain 'C' and (resid 340 through 360 )C340 - 360
17X-RAY DIFFRACTION17chain 'C' and (resid 361 through 379 )C361 - 379
18X-RAY DIFFRACTION18chain 'D' and (resid 570 through 725 )D570 - 725
19X-RAY DIFFRACTION19chain 'D' and (resid 726 through 853 )D726 - 853
20X-RAY DIFFRACTION20chain 'E' and (resid 422 through 436 )E422 - 436
21X-RAY DIFFRACTION21chain 'E' and (resid 437 through 446 )E437 - 446
22X-RAY DIFFRACTION22chain 'F' and (resid 422 through 436 )F422 - 436
23X-RAY DIFFRACTION23chain 'F' and (resid 437 through 446 )F437 - 446

+
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