[English] 日本語
Yorodumi
- PDB-6w8d: Structure of DNMT3A (R882H) in complex with CGT DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w8d
TitleStructure of DNMT3A (R882H) in complex with CGT DNA
Components
  • CGT DNA (25-MER)
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5)-methyltransferase 3A
KeywordsTRANSFERASE/DNA / DNA methylation / DNMT3A(R882H) / AML / epigenetics / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase ...retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / negative regulation of DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex / XY body / cellular response to ethanol / response to vitamin A / negative regulation of gene expression via chromosomal CpG island methylation / DNA metabolic process / negative regulation of gene expression, epigenetic / response to ionizing radiation / hepatocyte apoptotic process / male meiosis I / chromosome, centromeric region / catalytic complex / heterochromatin / enzyme activator activity / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / PRC2 methylates histones and DNA / response to cocaine / condensed nuclear chromosome / Defective pyroptosis / stem cell differentiation / placenta development / cellular response to amino acid stimulus / response to lead ion / euchromatin / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / transcription corepressor activity / response to estradiol / cellular response to hypoxia / methylation / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / DNMT3, cysteine rich ADD domain, GATA1-like 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 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / DNMT3, cysteine rich ADD domain, GATA1-like 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 3-like / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsAnteneh, H. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation.
Authors: Anteneh, H. / Fang, J. / Song, J.
History
DepositionMar 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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 3A
B: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3A
C: DNA (cytosine-5)-methyltransferase 3-like
E: CGT DNA (25-MER)
F: CGT DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8888
Polymers129,1196
Non-polymers7692
Water1,72996
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)205.560, 205.560, 89.505
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein DNA (cytosine-5)-methyltransferase 3A / DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / DNA methyltransferase HsaIIIA / M.HsaIIIA


Mass: 32696.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6K1, 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) / References: UniProt: Q9UJW3
#3: DNA chain CGT DNA (25-MER)


Mass: 7698.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium Citrate pH 4.2, 1% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.5 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.5 Å / Relative weight: 1
ReflectionResolution: 2.598→33.16 Å / Num. obs: 43419 / % possible obs: 98.9 % / Redundancy: 5.1 % / CC1/2: 0.998 / Net I/σ(I): 13.7
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 43403 / CC1/2: 0.636

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YX2

5yx2


Resolution: 2.598→33.159 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.21
RfactorNum. reflection% reflection
Rfree0.2526 1989 4.58 %
Rwork0.199 --
obs0.2015 43419 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 259.79 Å2 / Biso mean: 114.3489 Å2 / Biso min: 43.16 Å2
Refinement stepCycle: final / Resolution: 2.598→33.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7200 1020 52 96 8368
Biso mean--89.09 88.51 -
Num. residues----983
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.598-2.66250.39531390.3317293999
2.6625-2.73440.3331430.29382948100
2.7344-2.81480.32291420.28382959100
2.8148-2.90560.32771460.27132961100
2.9056-3.00940.34891400.26672956100
3.0094-3.12980.29611410.25722970100
3.1298-3.27220.2991440.2512930100
3.2722-3.44450.29421380.22332987100
3.4445-3.66010.26661420.21752965100
3.6601-3.94220.26561430.1992979100
3.9422-4.33820.26551430.17952953100
4.3382-4.96410.20251470.16142963100
4.9641-6.24740.20171400.19022962100
6.2474-33.1590.2381410.17252958100
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)
12.87970.3714-1.64274.3602-0.40924.67470.0395-0.7340.36280.4707-0.0496-0.4761-0.44120.5366-0.00730.6245-0.093-0.09130.6344-0.03850.562670.301830.8178-12.4262
22.86830.0699-1.1124.38611.10273.50620.15690.33380.3817-0.9279-0.2919-0.5488-0.74090.14560.20480.9431-0.01970.07270.56340.07870.647368.082839.0183-27.973
31.68740.3305-1.08724.4389-0.37513.9184-0.2250.5449-0.2621-1.4146-0.0448-0.81030.37380.03750.2121.05490.06720.24450.69890.01630.694167.933617.9679-32.9658
43.5056-0.4651.37170.0777-0.05043.92970.0130.1935-0.0222-2.0627-0.39250.1831.4789-1.1180.46581.917-0.1444-0.00051.2169-0.05480.777452.75868.9767-37.6411
52.12340.494-0.60284.571-0.75393.99830.044-0.0272-0.0222-0.3814-0.0723-0.37290.09270.2427-0.01990.65560.08360.10650.61410.00210.498866.291919.2664-22.4015
64.3520.1491-0.42811.25481.75172.5469-0.0146-1.48930.0237-2.32510.80910.7055-1.17810.226-1.34041.718-0.45520.19511.05570.01822.229580.740276.2746-19.4321
72.5894-0.3811.04192.4785-1.04091.18111.4541-0.23430.9762-0.88350.09850.3812-1.7351-0.3931-1.11212.2314-0.05030.2520.66980.11591.459167.901971.2176-32.6743
81.3517-1.4590.46274.6321-0.13784.7779-0.6234-0.278-0.2101-2.25940.0468-1.3435-0.550.18020.42671.91560.05450.38420.96180.0621.230274.873955.8995-35.747
91.0273-1.1566-1.41892.73990.63852.76820.49960.93721.4582-1.9929-0.53721.0787-0.8565-0.2849-0.04921.71770.2669-0.1560.75970.05621.462662.067161.8966-30.9368
102.15330.0563-0.62062.2395-1.29251.7754-0.112-0.38310.9862-0.384-0.1036-0.0766-0.51420.03120.21651.17970.0328-0.00910.6633-0.07471.161263.057359.7357-20.9123
113.62061.0440.17634.02630.2544.65790.57790.8599-0.89530.334-0.28531.62640.5910.5475-0.46821.1780.0112-0.05341.2879-0.25451.832946.77865.691-17.9775
122.34610.34540.97660.884-0.04121.52330.07020.04520.6734-0.4946-0.62120.1271-0.85140.13170.32932.0272-0.32510.10050.9144-0.292.019466.397876.9652-22.0767
132.7278-0.0145-0.03945.1003-0.4872.91850.0196-0.3254-0.30810.2054-0.02180.81220.4359-0.32630.0170.5739-0.1235-0.00890.58640.08480.532148.4677-15.1033-10.6117
141.71981.68730.17134.83921.98361.79770.105-0.195-0.10580.5226-0.21110.08070.4043-0.40720.08490.7037-0.04440.05990.74530.07730.450253.88671.33182.0681
151.91240.52360.27864.96010.91783.1208-0.0451-0.37440.19350.04680.07540.4956-0.0327-0.6390.0160.5108-0.00870.06450.74630.02250.418454.03154.3014-5.9563
160.79780.4525-0.40550.202-0.26341.2408-0.0577-0.3301-0.2819-0.77760.72650.44980.4277-0.8965-0.76420.9113-0.2553-0.10781.16830.17762.179426.7579-41.2867-6.2074
172.77771.04631.90680.46170.63112.1454-0.73780.6577-1.0880.42641.07690.067-0.30650.2455-0.72061.4053-0.49270.12671.49580.0761.79620.3657-42.6923-5.3146
181.3901-1.43530.22662.5611-0.44582.14430.0053-0.4983-1.24120.32210.23681.9790.3804-0.189-0.04810.8573-0.39410.01781.00910.21311.728931.2091-31.1885-5.8931
190.06050.0746-0.220.90830.51021.67610.35270.6503-2.4678-0.60590.41782.08910.4896-0.9239-0.59490.9224-0.4055-0.331.01280.26151.935127.7563-24.8159-17.7132
200.1602-0.01060.57970.46240.42991.7925-0.02050.137-0.48880.32560.1741.6338-0.2876-0.42670.10440.9648-0.2941-0.20291.06540.221.721121.5454-30.0156-23.9196
212.846-3.14582.30963.6683-2.44161.95581.39690.5475-0.7585-2.343-1.2403-1.04971.3999-0.3194-0.19021.5436-0.135-0.31261.0199-0.01192.168223.994-34.1718-25.0101
223.9389-0.9095-2.32841.30622.38924.7356-0.37690.58960.4793-0.4255-1.78110.6854-1.0212-1.32941.71091.4468-0.3441-0.47591.7125-0.08862.572411.1485-21.3891-20.2892
231.8528-0.0935-1.38821.06730.49731.2173-1.17661.0247-0.26550.40580.68450.45590.3777-0.48390.41591.703-0.6371-0.34361.3731-0.04971.76121.2654-44.6747-16.3695
243.29861.00560.65794.4616-0.06624.32980.7827-1.45271.19630.2901-0.70042.0804-1.9587-0.9466-0.27391.1360.01520.30031.6244-0.30951.756634.41345.3346-0.4371
251.9401-1.01190.44523.0717-0.86991.4696-0.38450.1506-0.7374-0.30210.39090.2195-0.5509-0.60150.05371.23510.1381-0.1511.6966-0.2081.71145.237626.1263-32.9372
262.5743-1.10212.08493.171-1.9699.73120.06331.5676-0.8429-1.19970.51630.21880.57080.4759-0.25231.8727-0.03880.05941.1861-0.0030.885156.922625.813-47.5947
278.12381.48340.18226.33960.70596.03951.063-1.5279-0.7418-1.6236-1.3323.44061.1675-3.51110.08091.1348-0.0293-0.29811.7781-0.24861.802443.171728.4292-30.9427
288.077-1.34193.90125.8932-1.5176.5789-1.71672.60190.0125-0.11870.53761.09380.5473-1.89921.26791.1731-0.31710.11542.0456-0.26851.931737.345715.5543-20.7494
291.0822-0.28041.60454.6666-1.3612.6272-0.6019-0.2179-0.65310.47830.26960.1135-0.81660.09970.19671.3802-0.13750.68951.6862-0.05942.191131.52885.55671.5698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 629 through 698 )A629 - 698
2X-RAY DIFFRACTION2chain 'A' and (resid 699 through 784 )A699 - 784
3X-RAY DIFFRACTION3chain 'A' and (resid 785 through 839 )A785 - 839
4X-RAY DIFFRACTION4chain 'A' and (resid 840 through 857 )A840 - 857
5X-RAY DIFFRACTION5chain 'A' and (resid 858 through 912 )A858 - 912
6X-RAY DIFFRACTION6chain 'B' and (resid 179 through 191 )B179 - 191
7X-RAY DIFFRACTION7chain 'B' and (resid 192 through 222 )B192 - 222
8X-RAY DIFFRACTION8chain 'B' and (resid 223 through 235 )B223 - 235
9X-RAY DIFFRACTION9chain 'B' and (resid 236 through 255 )B236 - 255
10X-RAY DIFFRACTION10chain 'B' and (resid 256 through 332 )B256 - 332
11X-RAY DIFFRACTION11chain 'B' and (resid 333 through 352 )B333 - 352
12X-RAY DIFFRACTION12chain 'B' and (resid 353 through 379 )B353 - 379
13X-RAY DIFFRACTION13chain 'D' and (resid 628 through 784 )D628 - 784
14X-RAY DIFFRACTION14chain 'D' and (resid 785 through 839 )D785 - 839
15X-RAY DIFFRACTION15chain 'D' and (resid 840 through 912 )D840 - 912
16X-RAY DIFFRACTION16chain 'C' and (resid 187 through 198 )C187 - 198
17X-RAY DIFFRACTION17chain 'C' and (resid 199 through 221 )C199 - 221
18X-RAY DIFFRACTION18chain 'C' and (resid 222 through 280 )C222 - 280
19X-RAY DIFFRACTION19chain 'C' and (resid 281 through 301 )C281 - 301
20X-RAY DIFFRACTION20chain 'C' and (resid 302 through 320 )C302 - 320
21X-RAY DIFFRACTION21chain 'C' and (resid 321 through 339 )C321 - 339
22X-RAY DIFFRACTION22chain 'C' and (resid 340 through 360 )C340 - 360
23X-RAY DIFFRACTION23chain 'C' and (resid 361 through 378 )C361 - 378
24X-RAY DIFFRACTION24chain 'E' and (resid 422 through 432 )E422 - 432
25X-RAY DIFFRACTION25chain 'E' and (resid 433 through 446 )E433 - 446
26X-RAY DIFFRACTION26chain 'F' and (resid 422 through 426 )F422 - 426
27X-RAY DIFFRACTION27chain 'F' and (resid 428 through 432 )F428 - 432
28X-RAY DIFFRACTION28chain 'F' and (resid 433 through 437 )F433 - 437
29X-RAY DIFFRACTION29chain 'F' and (resid 438 through 446 )F438 - 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