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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | CryoEM structure of Apo-DIM2 | |||||||||
![]() | sharpened map | |||||||||
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![]() | DNA methyltransferase / TRANSFERASE | |||||||||
Function / homology | ![]() DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / methylation / chromatin binding / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 Å | |||||||||
![]() | Song J / Shao Z | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM structure of Apo-DIM2 Authors: Song J / Shao Z | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 60 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.3 KB 16.3 KB | Display Display | ![]() |
Images | ![]() | 67.4 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() ![]() | 32.4 MB 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 733.5 KB | Display | ![]() |
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Full document | ![]() | 733 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9bapMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpened map
File | emd_44410_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_44410_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_44410_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Apo-DIM2
Entire | Name: Apo-DIM2 |
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Components |
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-Supramolecule #1: Apo-DIM2
Supramolecule | Name: Apo-DIM2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: DNA (cytosine-5-)-methyltransferase
Macromolecule | Name: DNA (cytosine-5-)-methyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 162.352641 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: S-ADENOSYL-L-HOMOCYSTEINE
Macromolecule | Name: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: SAH |
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Molecular weight | Theoretical: 384.411 Da |
Chemical component information | ![]() ChemComp-SAH: |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 529317 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |