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- EMDB-61999: Cryo-EM structure of USP7:DNMT1 complex; closed conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-61999
TitleCryo-EM structure of USP7:DNMT1 complex; closed conformation
Map data
Sample
  • Complex: DNMT1:USP7
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 7
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
  • Ligand: ZINC ION
KeywordsDNA methylation / deubiquitination / STRUCTURAL PROTEIN
Function / homology
Function and homology information


chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / regulation of telomere capping / regulation of establishment of protein localization to telomere / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase activity / monoubiquitinated protein deubiquitination / cellular response to bisphenol A ...chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / regulation of telomere capping / regulation of establishment of protein localization to telomere / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase activity / monoubiquitinated protein deubiquitination / cellular response to bisphenol A / regulation of retrograde transport, endosome to Golgi / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase / deubiquitinase activity / SUMOylation of DNA methylation proteins / DNA alkylation repair / female germ cell nucleus / STAT3 nuclear events downstream of ALK signaling / methyl-CpG binding / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of gluconeogenesis / pericentric heterochromatin / transcription-coupled nucleotide-excision repair / Nuclear events stimulated by ALK signaling in cancer / positive regulation of vascular associated smooth muscle cell proliferation / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / DNA methylation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / cellular response to amino acid stimulus / promoter-specific chromatin binding / regulation of circadian rhythm / NoRC negatively regulates rRNA expression / regulation of protein stability / PML body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / p53 binding / rhythmic process / Regulation of TP53 Degradation / chromosome / methylation / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / Ub-specific processing proteases / protein ubiquitination / nuclear body / negative regulation of gene expression / cysteine-type endopeptidase activity / DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / proteolysis / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. ...DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type 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 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 1 / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsNakamura N / Arita K
Funding support Japan, 7 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02392 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05294 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05741 Japan
Japan Society for the Promotion of Science (JSPS)24K01967 Japan
Japan Society for the Promotion of Science (JSPS)19H05285 Japan
Japan Society for the Promotion of Science (JSPS)21H00272 Japan
Japan Society for the Promotion of Science (JSPS)24K02001 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of activation/inactivation forms of UPS7 bound to DNMT1
Authors: Nakamura N / Yoshimi S / Kikuchi A / Kori S / Onoda H / Nakanishi M / Nishiyama A / Arita K
History
DepositionOct 18, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61999.png

Downloads & links

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Map

FileDownload / File: emd_61999.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 180 pix.
= 248.544 Å		1.38 Å/pix.
x 180 pix.
= 248.544 Å		1.38 Å/pix.
x 180 pix.
= 248.544 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0692
Minimum - Maximum-0.7784386 - 1.3271731
Average (Standard dev.)0.0011956665 (±0.03245877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 248.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61999_msk_1.map
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Additional map: #1

Fileemd_61999_additional_1.map
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Half map: #2

Fileemd_61999_half_map_1.map
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Half map: #1

Fileemd_61999_half_map_2.map
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Sample components

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Entire : DNMT1:USP7

EntireName: DNMT1:USP7
Components
  • Complex: DNMT1:USP7
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 7
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 1
  • Ligand: ZINC ION

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Supramolecule #1: DNMT1:USP7

SupramoleculeName: DNMT1:USP7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ubiquitin carboxyl-terminal hydrolase 7

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 128.884203 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMNHQQ QQQQQKAGEQ QLSEPEDMEM EAGDTDDPPR ITQNPVINGN VALSDGHNTA EEDMEDDTSW RSEATFQFTV ERFSRLSES VLSPPCFVRN LPWKIMVMPR FYPDRPHQKS VGFFLQCNAE SDSTSWSCHA QAVLKIINYR DDEKSFSRRI S HLFFHKEN ...String:
GPLGSMNHQQ QQQQQKAGEQ QLSEPEDMEM EAGDTDDPPR ITQNPVINGN VALSDGHNTA EEDMEDDTSW RSEATFQFTV ERFSRLSES VLSPPCFVRN LPWKIMVMPR FYPDRPHQKS VGFFLQCNAE SDSTSWSCHA QAVLKIINYR DDEKSFSRRI S HLFFHKEN DWGFSNFMAW SEVTDPEKGF IDDDKVTFEV FVQADAPHGV AWDSKKHTGY VGLKNQGATC YMNSLLQTLF FT NQLRKAV YMMPTEGDDS SKSVPLALQR VFYELQHSDK PVGTKKLTKS FGWETLDSFM QHDVQELCRV LLDNVENKMK GTC VEGTIP KLFRGKMVSY IQCKEVDYRS DRREDYYDIQ LSIKGKKNIF ESFVDYVAVE QLDGDNKYDA GEHGLQEAEK GVKF LTLPP VLHLQLMRFM YDPQTDQNIK INDRFEFPEQ LPLDEFLQKT DPKDPANYIL HAVLVHSGDN HGGHYVVYLN PKGDG KWCK FDDDVVSRCT KEEAIEHNYG GHDDDLSVRH CTNAYMLVYI RESKLSEVLQ AVTDHDIPQQ LVERLQEEKR IEAQKR KER QEAHLYMQVQ IVAEDQFCGH QGNDMYDEEK VKYTVFKVLK NSSLAEFVQS LSQTMGFPQD QIRLWPMQAR SNGTKRP AM LDNEADGNKT MIELSDNENP WTIFLETVDP ELAASGATLP KFDKDHDVML FLKMYDPKTR SLNYCGHIYT PISCKIRD L LPVMCDRAGF IQDTSLILYE EVKPNLTERI QDYDVSLDKA LDELMDGDII VFQKDDPEND NSELPTAKEY FRDLYHRVD VIFCDKTIPN DPGFVVTLSN RMNYFQVAKT VAQRLNTDPM LLQFFKSQGY RDGPGNPLRH NYEGTLRDLL QFFKPRQPKK LYYQQLKMK ITDFENRRSF KCIWLNSQFR EEEITLYPDK HGCVRDLLEE CKKAVELGEK ASGKLRLLEI VSYKIIGVHQ E DELLECLS PATSRTFRIE EIPLDQVDID KENEMLVTVA HFHKEVFGTF GIPFLLRIHQ GEHFREVMKR IQSLLDIQEK EF EKFKFAI VMMGRHQYIN EDEYEVNLKD FEPQPGNMSH PRPWLGLDHF NKAPKRSRYT YLEKAIKIHN

UniProtKB: Ubiquitin carboxyl-terminal hydrolase 7

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Macromolecule #2: DNA (cytosine-5)-methyltransferase 1

MacromoleculeName: DNA (cytosine-5)-methyltransferase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 143.559531 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPPTTPKCIQ CGQYLDDPDL KYGQHPPDAV DEPQMLTNEK LSIFDANESG FESYEALPQH KLTCFSVYCK HGHLCPIDTG LIEKNIELF FSGSAKPIYD DDPSLEGGVN GKNLGPINEW WITGFDGGEK ALIGFSTSFA EYILMDPSPE YAPIFGLMQE K IYISKIVV ...String:
GPPTTPKCIQ CGQYLDDPDL KYGQHPPDAV DEPQMLTNEK LSIFDANESG FESYEALPQH KLTCFSVYCK HGHLCPIDTG LIEKNIELF FSGSAKPIYD DDPSLEGGVN GKNLGPINEW WITGFDGGEK ALIGFSTSFA EYILMDPSPE YAPIFGLMQE K IYISKIVV EFLQSNSDST YEDLINKIET TVPPSGLNLN RFTEDSLLRH AQFVVEQVES YDEAGDSDEQ PIFLTPCMRD LI KLAGVTL GQRRAQARRQ TIRHSTREKD RGPTKATTTK LVYQIFDTFF AEQIEKDDRE DKENAFKRRR CGVCEVCQQP ECG KCKACK DMVKFGGSGR SKQACQERRC PNMAMKEADD DEEVDDNIPE MPSPKKMHQG KKKKQNKNRI SWVGEAVKTD GKKS YYKKV CIDAETLEVG DCVSVIPDDS SKPLYLARVT ALWEDSSNGQ MFHAHWFCAG TDTVLGATSD PLELFLVDEC EDMQL SYIH SKVKVIYKAP SENWAMEGGM DPESLLEGDD GKTYFYQLWY DQDYARFESP PKTQPTEDNK FKFCVSCARL AEMRQK EIP RVLEQLEDLD SRVLYYSATK NGILYRVGDG VYLPPEAFTF NIKLSSPVKR PRKEPVDEDL YPEHYRKYSD YIKGSNL DA PEPYRIGRIK EIFCPKKSNG RPNETDIKIR VNKFYRPENT HKSTPASYHA DINLLYWSDE EAVVDFKAVQ GRCTVEYG E DLPECVQVYS MGGPNRFYFL EAYNAKSKSF EDPPNHARSP GNKGKGKGKG KGKPKSQACE PSEPEIEIKL PKLRTLDVF SGCGGLSEGF HQAGISDTLW AIEMWDPAAQ AFRLNNPGST VFTEDCNILL KLVMAGETTN SRGQRLPQKG DVEMLCGGPP CQGFSGMNR FNSRTYSKFK NSLVVSFLSY CDYYRPRFFL LENVRNFVSF KRSMVLKLTL RCLVRMGYQC TFGVLQAGQY G VAQTRRRA IILAAAPGEK LPLFPEPLHV FAPRACQLSV VVDDKKFVSN ITRLSSGPFR TITVRDTMSD LPEVRNGASA LE ISYNGEP QSWFQRQLRG AQYQPILRDH ICKDMSALVA ARMRHIPLAP GSDWRDLPNI EVRLSDGTMA RKLRYTHHDR KNG RSSSGA LRGVCSCVEA GKACDPAARQ FNTLIPWCLP HTGNRHNHWA GLYGRLEWDG FFSTTVTNPE PMGKQGRVLH PEQH RVVSV RECARSQGFP DTYRLFGNIL DKHRQVGNAV PPPLAKAIGL EIKLCMLAKA RESASAKIKE EEAAKD

UniProtKB: DNA (cytosine-5)-methyltransferase 1

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / 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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.918 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 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: PDB ENTRY
PDB model - PDB ID:

4wxx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58485
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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