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- EMDB-75875: Cryo-EM consensus map of human DNMT3A homo-hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-75875
TitleCryo-EM consensus map of human DNMT3A homo-hexamer
Map dataSharpened map
Sample
  • Complex: DNA (cytosine-5)-methyltransferase 3A
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
KeywordsDNA (cytosine-5-)-methyltransferase / TRANSFERASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsSong J / Lu J / Chen J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of human DNMT3A homo-hexamer
Authors: Song J / Lu J / Chen J
History
DepositionMar 5, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75875.png

Downloads & links

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Map

FileDownload / File: emd_75875.map.gz / Format: CCP4 / Size: 87.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 284 pix.
= 370.109 Å		1.3 Å/pix.
x 284 pix.
= 370.109 Å		1.3 Å/pix.
x 284 pix.
= 370.109 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3032 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0337
Minimum - Maximum-0.35331511 - 0.750231
Average (Standard dev.)-0.00012204219 (±0.015198775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions284284284
Spacing284284284
CellA=B=C: 370.1088 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_75875_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_75875_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_75875_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA (cytosine-5)-methyltransferase 3A

EntireName: DNA (cytosine-5)-methyltransferase 3A
Components
  • Complex: DNA (cytosine-5)-methyltransferase 3A
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A

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Supramolecule #1: DNA (cytosine-5)-methyltransferase 3A

SupramoleculeName: DNA (cytosine-5)-methyltransferase 3A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA (cytosine-5)-methyltransferase 3A

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: SEPEYEDGRG FGIGELVWGK LRGFSWWPGR IVSWWMTGRS RAAEGTRWVM WFGDGKFSVV CVEKLMPLSS FCSAFHQATY NKQPMYRKAI YEVLQVASSR AGKLFPVCHD SDESDTAKAV EVQNKPMIEW ALGGFQPSGP KGLEPPEEEK NPYKEVYTDM WVEPEAAAYA ...String:
SEPEYEDGRG FGIGELVWGK LRGFSWWPGR IVSWWMTGRS RAAEGTRWVM WFGDGKFSVV CVEKLMPLSS FCSAFHQATY NKQPMYRKAI YEVLQVASSR AGKLFPVCHD SDESDTAKAV EVQNKPMIEW ALGGFQPSGP KGLEPPEEEK NPYKEVYTDM WVEPEAAAYA PPPPAKKPRK STAEKPKVKE IIDERTRERL VYEVRQKCRN IEDICISCGS LNVTLEHPLF VGGMCQNCKN CFLECAYQYD DDGYQSYCTI CCGGREVLMC GNNNCCRCFC VECVDLLVGP GAAQAAIKED PWNCYMCGHK GTYGLLRRRE DWPSRLQMFF ANNHDQEFDP PKVYPPVPAE KRKPIRVLSL FDGIATGLLV LKDLGIQVDR YIASEVCEDS ITVGMVRHQG KIMYVGDVRS VTQKHIQEWG PFDLVIGGSP CNDLSIVNPA RKGLYEGTGR LFFEFYRLLH DARPKEGDDR PFFWLFENVV AMGVSDKRDI SRFLESNPVM IDAKEVSAAH RARYFWGNLP GMNRPLASTV NDKLELQECL EHGRIAKFSK VRTITTRSNS IKQGKDQHFP VFMNEKEDIL WCTEMERVFG FPVHYTDVSN MSRLARQRLL GRSWSVPVIR HLFAPLKEYF ACVSEPEYED GRGFGIGELV WGKLRGFSWW PGRIVSWWMT GRSRAAEGTR WVMWFGDGKF SVVCVEKLMP LSSFCSAFHQ ATYNKQPMYR KAIYEVLQVA SSRAGKLFPV CHDSDESDTA KAVEVQNKPM IEWALGGFQP SGPKGLEPPE EEKNPYKEVY TDMWVEPEAA AYAPPPPAKK PRKSTAEKPK VKEIIDERTR ERLVYEVRQK CRNIEDICIS CGSLNVTLEH PLFVGGMCQN CKNCFLECAY QYDDDGYQSY CTICCGGREV LMCGNNNCCR CFCVECVDLL VGPGAAQAAI KEDPWNCYMC GHKGTYGLLR RREDWPSRLQ MFFANNHDQE FDPPKVYPPV PAEKRKPIRV LSLFDGIATG LLVLKDLGIQ VDRYIASEVC EDSITVGMVR HQGKIMYVGD VRSVTQKHIQ EWGPFDLVIG GSPCNDLSIV NPARKGLYEG TGRLFFEFYR LLHDARPKEG DDRPFFWLFE NVVAMGVSDK RDISRFLESN PVMIDAKEVS AAHRARYFWG NLPGMNRPLA STVNDKLELQ ECLEHGRIAK FSKVRTITTR SNSIKQGKDQ HFPVFMNEKE DILWCTEMER VFGFPVHYTD VSNMSRLARQ RLLGRSWSVP VIRHLFAPLK EYFACVSEPE YEDGRGFGIG ELVWGKLRGF SWWPGRIVSW WMTGRSRAAE GTRWVMWFGD GKFSVVCVEK LMPLSSFCSA FHQATYNKQP MYRKAIYEVL QVASSRAGKL FPVCHDSDES DTAKAVEVQN KPMIEWALGG FQPSGPKGLE PPEEEKNPYK EVYTDMWVEP EAAAYAPPPP AKKPRKSTAE KPKVKEIIDE RTRERLVYEV RQKCRNIEDI CISCGSLNVT LEHPLFVGGM CQNCKNCFLE CAYQYDDDGY QSYCTICCGG REVLMCGNNN CCRCFCVECV DLLVGPGAAQ AAIKEDPWNC YMCGHKGTYG LLRRREDWPS RLQMFFANNH DQEFDPPKVY PPVPAEKRKP IRVLSLFDGI ATGLLVLKDL GIQVDRYIAS EVCEDSITVG MVRHQGKIMY VGDVRSVTQK HIQEWGPFDL VIGGSPCNDL SIVNPARKGL YEGTGRLFFE FYRLLHDARP KEGDDRPFFW LFENVVAMGV SDKRDISRFL ESNPVMIDAK EVSAAHRARY FWGNLPGMNR PLASTVNDKL ELQECLEHGR IAKFSKVRTI TTRSNSIKQG KDQHFPVFMN EKEDILWCTE MERVFGFPVH YTDVSNMSRL ARQRLLGRSW SVPVIRHLFA PLKEYFACVS EPEYEDGRGF GIGELVWGKL RGFSWWPGRI VSWWMTGRSR AAEGTRWVMW FGDGKFSVVC VEKLMPLSSF CSAFHQATYN KQPMYRKAIY EVLQVASSRA GKLFPVCHDS DESDTAKAVE VQNKPMIEWA LGGFQPSGPK GLEPPEEEKN PYKEVYTDMW VEPEAAAYAP PPPAKKPRKS TAEKPKVKEI IDERTRERLV YEVRQKCRNI EDICISCGSL NVTLEHPLFV GGMCQNCKNC FLECAYQYDD DGYQSYCTIC CGGREVLMCG NNNCCRCFCV ECVDLLVGPG AAQAAIKEDP WNCYMCGHKG TYGLLRRRED WPSRLQMFFA NNHDQEFDPP KVYPPVPAEK RKPIRVLSLF DGIATGLLVL KDLGIQVDRY IASEVCEDSI TVGMVRHQGK IMYVGDVRSV TQKHIQEWGP FDLVIGGSPC NDLSIVNPAR KGLYEGTGRL FFEFYRLLHD ARPKEGDDRP FFWLFENVVA MGVSDKRDIS RFLESNPVMI DAKEVSAAHR ARYFWGNLPG MNRPLASTVN DKLELQECLE HGRIAKFSKV RTITTRSNSI KQGKDQHFPV FMNEKEDILW CTEMERVFGF PVHYTDVSNM SRLARQRLLG RSWSVPVIRH LFAPLKEYFA CVSEPEYEDG RGFGIGELVW GKLRGFSWWP GRIVSWWMTG RSRAAEGTRW VMWFGDGKFS VVCVEKLMPL SSFCSAFHQA TYNKQPMYRK AIYEVLQVAS SRAGKLFPVC HDSDESDTAK AVEVQNKPMI EWALGGFQPS GPKGLEPPEE EKNPYKEVYT DMWVEPEAAA YAPPPPAKKP RKSTAEKPKV KEIIDERTRE RLVYEVRQKC RNIEDICISC GSLNVTLEHP LFVGGMCQNC KNCFLECAYQ YDDDGYQSYC TICCGGREVL MCGNNNCCRC FCVECVDLLV GPGAAQAAIK EDPWNCYMCG HKGTYGLLRR REDWPSRLQM FFANNHDQEF DPPKVYPPVP AEKRKPIRVL SLFDGIATGL LVLKDLGIQV DRYIASEVCE DSITVGMVRH QGKIMYVGDV RSVTQKHIQE WGPFDLVIGG SPCNDLSIVN PARKGLYEGT GRLFFEFYRL LHDARPKEGD DRPFFWLFEN VVAMGVSDKR DISRFLESNP VMIDAKEVSA AHRARYFWGN LPGMNRPLAS TVNDKLELQE CLEHGRIAKF SKVRTITTRS NSIKQGKDQH FPVFMNEKED ILWCTEMERV FGFPVHYTDV SNMSRLARQR LLGRSWSVPV IRHLFAPLKE YFACVSEPEY EDGRGFGIGE LVWGKLRGFS WWPGRIVSWW MTGRSRAAEG TRWVMWFGDG KFSVVCVEKL MPLSSFCSAF HQATYNKQPM YRKAIYEVLQ VASSRAGKLF PVCHDSDESD TAKAVEVQNK PMIEWALGGF QPSGPKGLEP PEEEKNPYKE VYTDMWVEPE AAAYAPPPPA KKPRKSTAEK PKVKEIIDER TRERLVYEVR QKCRNIEDIC ISCGSLNVTL EHPLFVGGMC QNCKNCFLEC AYQYDDDGYQ SYCTICCGGR EVLMCGNNNC CRCFCVECVD LLVGPGAAQA AIKEDPWNCY MCGHKGTYGL LRRREDWPSR LQMFFANNHD QEFDPPKVYP PVPAEKRKPI RVLSLFDGIA TGLLVLKDLG IQVDRYIASE VCEDSITVGM VRHQGKIMYV GDVRSVTQKH IQEWGPFDLV IGGSPCNDLS IVNPARKGLY EGTGRLFFEF YRLLHDARPK EGDDRPFFWL FENVVAMGVS DKRDISRFLE SNPVMIDAKE VSAAHRARYF WGNLPGMNRP LASTVNDKLE LQECLEHGRI AKFSKVRTIT TRSNSIKQGK DQHFPVFMNE KEDILWCTEM ERVFGFPVHY TDVSNMSRLA RQRLLGRSWS VPVIRHLFAP LKEYFACV

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
Details: 20 mM Hepes-NaOH (pH 7.2), 250 mM NaCl, 2.5% (v/v) glycerol, and 5 mM DTT
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 197622
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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