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- EMDB-44410: CryoEM structure of Apo-DIM2 -

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Basic information

Entry
Database: EMDB / ID: EMD-44410
TitleCryoEM structure of Apo-DIM2
Map datasharpened map
Sample
  • Complex: Apo-DIM2
    • Protein or peptide: DNA (cytosine-5-)-methyltransferase
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION
KeywordsDNA methyltransferase / TRANSFERASE
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / methylation / chromatin binding / DNA binding / nucleus
Similarity search - Function
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 / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology (BAH) domain / BAH domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA (cytosine-5-)-methyltransferase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsSong J / Shao Z
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: CryoEM structure of Apo-DIM2
Authors: Song J / Shao Z
History
DepositionApr 4, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44410.png

Downloads & links

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Map

FileDownload / File: emd_44410.map.gz / Format: CCP4 / Size: 64 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.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.101
Minimum - Maximum-1.2350203 - 2.0222592
Average (Standard dev.)-0.00036929388 (±0.029075518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_44410_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 A

Fileemd_44410_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_44410_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo-DIM2

EntireName: Apo-DIM2
Components
  • Complex: Apo-DIM2
    • Protein or peptide: DNA (cytosine-5-)-methyltransferase
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION

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Supramolecule #1: Apo-DIM2

SupramoleculeName: Apo-DIM2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neurospora crassa (fungus)

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

MacromoleculeName: DNA (cytosine-5-)-methyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 162.352641 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMDSPDRSH GGMFIDVPAE TMGFQEDYLD MFASVLSQGL AKEGDYAHHQ PLPAGKEECL EPIAVATTIT PSPDDPQLQL QLELEQQFQ TESGLNGVDP APAPESEDEA DLPDGFSDES PDDDFVVQRS KHITVDLPVS TLINPRSTFQ RIDENDNLVP P PQSTPERV ...String:
GSMDSPDRSH GGMFIDVPAE TMGFQEDYLD MFASVLSQGL AKEGDYAHHQ PLPAGKEECL EPIAVATTIT PSPDDPQLQL QLELEQQFQ TESGLNGVDP APAPESEDEA DLPDGFSDES PDDDFVVQRS KHITVDLPVS TLINPRSTFQ RIDENDNLVP P PQSTPERV AVEDLLKAAK AAGKNKEDYI EFELHDFNFY VNYAYHPQEM RPIQLVATKV LHDKYYFDGV LKYGNTKHYV TG MQVLELP VGNYGASLHS VKGQIWVRSK HNAKKEIYYL LKKPAFEYQR YYQPFLWIAD LGKHVVDYCT RMVERKREVT LGC FKSDFI QWASKAHGKS KAFQNWRAQH PSDDFRTSVA ANIGYIWKEI NGVAGAKRAA GDQLFRELMI VKPGQYFRQE VPPG PVVTE GDRTVAATIV TPYIKECFGH MILGKVLRLA GEDAEKEKEV KLAKRLKIEN KNATKADTKD DMKNDTATES LPTPL RSLP VQVLEATPIE SDIVSIVSSD LPPSENNPPP LTNGSVKPKA KANPKPKPST QPLHAAHVKY LSQELVNKIK VGDVIS TPR DDSSNTDTKW KPTDTDDHRW FGLVQRVHTA KTKSSGRGLN SKSFDVIWFY RPEDTPCCAM KYKWRNELFL SNHCTCQ EG HHARVKGNEV LAVHPVDWFG TPESNKGEFF VRQLYESEQR RWITLQKDHL TCYHNQPPKP PTAPYKPGDT VLATLSPS D KFSDPYEVVE YFTQGEKETA FVRLRKLLRR RKVDRQDAPA NELVYTEDLV DVRAERIVGK CIMRCFRPDE RVPSPYDRG GTGNMFFITH RQDHGRCVPL DTLPPTLRQG FNPLGNLGKP KLRGMDLYCG GGNFGRGLEE GGVVEMRWAN DIWDKAIHTY MANTPDPNK TNPFLGSVDD LLRLALEGKF SDNVPRPGEV DFIAAGSPCP GFSLLTQDKK VLNQVKNQSL VASFASFVDF Y RPKYGVLE NVSGIVQTFV NRKQDVLSQL FCALVGMGYQ AQLILGDAWA HGAPQSRERV FLYFAAPGLP LPDPPLPSHS HY RVKNRNI GFLCNGESYV QRSFIPTAFK FVSAGEGTAD LPKIGDGKPD ACVRFPDHRL ASGITPYIRA QYACIPTHPY GMN FIKAWN NGNGVMSKSD RDLFPSEGKT RTSDASVGWK RLNPKTLFPT VTTTSNPSDA RMGPGLHWDE DRPYTVQEMR RAQG YLDEE VLVGRTTDQW KLVGNSVSRH MALAIGLKFR EAWLGTLYDE SAVVATATAT ATTAAAVGVT VPVMEEPGIG TTESS RPSR SPVHTAVDLD DSKSERSRST TPATVLSTSS AAGDGSANAA GLEDDDNDDM EMMEVTRKRS SPAVDEEGMR PSKVQK VEV TVASPASRRS SRQASRNPTA SPSSKASKAT THEAPAPEEL ESDAESYSET YDKEGFDGDY HSGHEDQYSE EDEEEEY AE PETMTVNGMT IVKL

UniProtKB: DNA (cytosine-5-)-methyltransferase

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Macromolecule #2: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 529317
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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