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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24292 | |||||||||
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Title | Cryo-EM structure of DNMT5 in apo state | |||||||||
![]() | Cryo-EM structure of DNMT5 in apo state | |||||||||
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![]() | Cytosine-5 methyltransferase / SNF2 ATPase / TRANSFERASE | |||||||||
Function / homology | ![]() ATP-dependent DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent heterochromatin formation / ATP-dependent chromatin remodeler activity / nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromosome / methylation / sequence-specific DNA binding / chromatin binding ...ATP-dependent DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent heterochromatin formation / ATP-dependent chromatin remodeler activity / nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromosome / methylation / sequence-specific DNA binding / chromatin binding / ATP hydrolysis activity / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Wang J / Patel DJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance. Authors: Juncheng Wang / Sandra Catania / Chongyuan Wang / M Jason de la Cruz / Beiduo Rao / Hiten D Madhani / Dinshaw J Patel / ![]() Abstract: Epigenetic evolution occurs over million-year timescales in Cryptococcus neoformans and is mediated by DNMT5, the first maintenance type cytosine methyltransferase identified in the fungal or protist ...Epigenetic evolution occurs over million-year timescales in Cryptococcus neoformans and is mediated by DNMT5, the first maintenance type cytosine methyltransferase identified in the fungal or protist kingdoms, the first dependent on adenosine triphosphate (ATP), and the most hemimethyl-DNA-specific enzyme known. To understand these novel properties, we solved cryo-EM structures of CnDNMT5 in three states. These studies reveal an elaborate allosteric cascade in which hemimethylated DNA binding first activates the SNF2 ATPase domain by a large rigid body rotation while the target cytosine partially flips out of the DNA duplex. ATP binding then triggers striking structural reconfigurations of the methyltransferase catalytic pocket to enable cofactor binding, completion of base flipping, and catalysis. Bound unmethylated DNA does not open the catalytic pocket and is instead ejected upon ATP binding, driving high fidelity. This unprecedented chaperone-like, enzyme-remodeling role of the SNF2 ATPase domain illuminates how energy is used to enable faithful epigenetic memory. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 60 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.3 KB 13.3 KB | Display Display | ![]() |
Images | ![]() | 64.4 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r76MC ![]() 7r77C ![]() 7r78C ![]() 7t02C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of DNMT5 in apo state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : DNMT5
Entire | Name: DNMT5 |
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Components |
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-Supramolecule #1: DNMT5
Supramolecule | Name: DNMT5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 260 KDa |
-Macromolecule #1: DNA repair protein Rad8
Macromolecule | Name: DNA repair protein Rad8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 |
Molecular weight | Theoretical: 263.811656 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMGSGD DWYEIDYIAD SRVIRRKGRQ ILQYLIHWAG YAVHERTWED EDGIGGEDCA LVQEFYRKN PGKPRLSPSS VRKEVKLARM VEVVITTRRI DGKSRAASST DQPSPHRLGI TSPQANNIGG EDPNPSLTRR P VRSTVSEI ...String: MSYYHHHHHH DYDIPTTENL YFQGAMGSGD DWYEIDYIAD SRVIRRKGRQ ILQYLIHWAG YAVHERTWED EDGIGGEDCA LVQEFYRKN PGKPRLSPSS VRKEVKLARM VEVVITTRRI DGKSRAASST DQPSPHRLGI TSPQANNIGG EDPNPSLTRR P VRSTVSEI AKRPTSKKVH PNKKCKASSD DESDFVFEEG EWDEDEDDDN DVDFRSSEDD EDDEQERSAE EPESDEEIIK PA KKTKSSL PKAKLRPKPA NLGGFVTGVR PLNQGLDIKA AVRNMSDDLP PISDIEAMFD HLVSRIPDIV ELVRQLNGRK LRV ATMCSG TESPLLALNM IAKAIKAQHG LTLAFEHVFS CEIEPFKQAY IERNFTPPIL FRDVTELGKK RAHTAYGSMV DVPG DVDIL IAGTSCVDYS NLNNVQQDID ANGESGRTFR GMLQWVKKHQ PPIVILENVC NAPWDKVVEY FGQIDYDAQY TRLDT KEFY IPHTRTRVYL FATPSSSESD DLPEKWAQTV KDLRRPWSSP FEAFLLHTDD PNIHRARLEL ASARAQTDGT SRKTTD WNR CESRHQRARQ DEALGLLRPL TSWQEAGVCK GLDWTWNDWL LAQTERVVDL LEISTLRMAK DGIDSGFKAC IWNVSQN VD RQTGSSKTAL APCLTPNMIP WVTIRGGPVT GREALALQGI PVRELLLTSE NEDQLADLAG NAMTTTVVGS AMIAALKV A CHKITEGANP EKEAALILEK EAVDDEQVAN RIIGEDYLEH HDLDLAKVTK SNLSEILDLA CRSSRHCQCE GQSGTAPNI LECQECSYRA CKSCGGRPEH VYAPCANQRV EPAEFEKRFK GLLPMRVRIA GLTDQCLNAV RKAAEKSNKG SVNDNDWQLW STALLEGIH DAEFRFRYLK RQSTWTAVYE ARRAMLSLVL RNQIPEWRLT IKAPASEPNN SQLRALLLHP VARLQIDIAG Q DVLCGPWE LCIPSMKTID IEITGKGELL PSWQASLGLQ GPFANTTRWS EVEISLQAED ENTLDRKLSG TYQLLPRCGQ AM SSLHKKR PDLSDDGLPQ LYFFLDPTRC GESREDRYVF STSTERLDYG TERPVIARLD SHWREGNEKQ RKVKLDVSGA WVK CPEAHL TAIGGDDIAV VANDAAANEI HRDRATFAIP SSASAISASL TTEGCSHAMA LLSCRVPLDP THSESMWRRG AWAE IDLSH QGNTTFANLA WITERLPPLD GLKNWAHIAD DVSEHVCERC APRPPKIHWI KREGKANKKG NKTKSTIIAF EDKLE AGQY EHALKHRPSP FVVQLRLDQD IGSFRIGLNI VSLAHRALSR LPPTTSEHKI SLSWRLTPGH VTESPQPRRV FILPSN KQD PENSQPEAFK LPLRKEQLRS LWWMLEQEKA TGKTHTFVEE EISESLLPAV GWRAEGKAER PVMVRGGVIA DQVGYGK TV ISIALVAQTL SLPAPEPATP GLIDLKATLI VVPGHLSKQW PNEIARFTGS MFKVIVIQGM KDLQEKTIAE LGKADIIV M ASEIFESDVY WSRLEYLSAQ PREWLHDTQG GRFFCDRLDA AMESLVSQTK ILKEKGSEAA MRAMEDKKKS LVDNVGSKK EVHTAVNFGK RMKGQAYRDK HDSDSKAKPI TKEELERWEA SEDEDDDENS KTYIPIPKFH SFTGSESIFS ASVKKDYKLL PNPVLHMFR FRRVIADEFT YLQKKSLAAV LRLSSSYRWI LSGTPPVSDF AAIRSIATFM GIHLGVEDDG EGDVQYQKAR A KDQTQAEK FHAFREVHSR AWHNRRDELA QEFLNVFVRQ NIAEIEDIPT VEHIHTFKLP ASEGAVYLEL EHHLQALEMQ AR KETKFKN VSQGDRNARL EEALSDSKTA EEALLKRCCH FTLDLSDKTQ DAKSAQEACD HITSARARQL LACQEDLSRS VNQ AIALHG WIKKKGGFSK NDDERQPFAE WIAFSSNISK HQGDIEAARI LLKVIEKCGV KDGNIPPSPS DKQSPSIASG AKMD DVKWQ LREQTHLLRK LVKELVARVR SLRFFEVVRK IQKGKSDAQI VLESSECGHK PSTNPDIEMA ILSCCGHVAC HKCMR KAAA SQRCVKSGEC QAAVRPTNIV KVSSLGVEGE LSSGRYGAKL EHLVNLIHSI PKNERVLVFL QWEDLAGKVS EALSAG RIP HVTLSGSAKS RANTLDRFQS TNADSARVLL LKMNDASAAG SNLTTANHAV FLGPLFTNSL FNYRAVETQA IGRVRRY GQ QKKVHIHRLL ALDTIDMTIF NARRTELKEK TDWEEIPQEE YKGRGSSISM TNEKRTPTLT VKSNPFKRSS SWALASSF R SKKRSMEARD AEGVSDDDEN SELSDII UniProtKB: DNA (cytosine-5-)-methyltransferase DMT5 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 5 / 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
Concentration | 0.19 mg/mL |
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Buffer | pH: 8 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 370.0 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 47262 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 22500 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72216 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7r76: |