Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form). Determined by electron microscopy at 2.23 Å resolution. Released 30 Nov 2022.
Explore 7XIB in 3D Show helices and sheets RCSB PDB PDBe
7XIB contains 47 α-helices and 46 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 615-617 | 3 | |
| β-strand | 618 | 1 | 1 |
| α-helix | 619 | 1 | |
| α-helix | 622-628 | 7 | |
| β-strand | 636 | 1 | 1 |
| β-strand | 762-765 | 4 | 2 |
| β-strand | 775-781 | 7 | 2 |
| β-strand | 791-799 | 9 | 2 |
| α-helix | 800-802 | 3 | |
| α-helix | 806-808 | 3 | |
| β-strand | 813-824 | 12 | 2 |
| β-strand | 828-831 | 4 | 2 |
| β-strand | 834-836 | 3 | 2 |
| α-helix | 838-840 | 3 | |
| α-helix | 843-845 | 3 | |
| β-strand | 863-870 | 8 | 2 |
| β-strand | 875-877 | 3 | 2 |
| α-helix | 878-880 | 3 | |
| α-helix | 894-903 | 10 | |
| β-strand | 909-916 | 8 | 3 |
| β-strand | 920-928 | 9 | 3 |
| β-strand | 931-934 | 4 | 3 |
| β-strand | 938-941 | 4 | 3 |
| α-helix | 972-974 | 3 | |
| α-helix | 987-989 | 3 | |
| β-strand | 992-1002 | 11 | 3 |
| β-strand | 1003 | 1 | 4 |
| β-strand | 1009 | 1 | 4 |
| β-strand | 1015-1022 | 8 | 3 |
| α-helix | 1024-1026 | 3 | |
| α-helix | 1031-1034 | 4 | |
| β-strand | 1041-1052 | 12 | 3 |
| α-helix | 1053-1055 | 3 | |
| β-strand | 1058-1064 | 7 | 3 |
| α-helix | 1065-1067 | 3 | |
| α-helix | 1072-1076 | 5 | |
| β-strand | 1082-1090 | 9 | 3 |
| β-strand | 1095-1097 | 3 | 3 |
| α-helix | 1098-1100 | 3 | |
| α-helix | 1137-1138 | 2 | |
| β-strand | 1139-1144 | 6 | 2 |
| α-helix | 1150-1157 | 8 | |
| β-strand | 1161-1167 | 7 | 2 |
| α-helix | 1171-1180 | 10 | |
| β-strand | 1185-1187 | 3 | 2 |
| α-helix | 1191-1198 | 8 | |
| β-strand | 1219-1222 | 4 | 2 |
| α-helix | 1239-1245 | 7 | |
| α-helix | 1247-1258 | 12 | |
| β-strand | 1262-1268 | 7 | 2 |
| α-helix | 1269-1272 | 4 | |
| α-helix | 1274-1290 | 17 | |
| β-strand | 1293-1300 | 8 | 2 |
| α-helix | 1301-1304 | 4 | |
| β-strand | 1308 | 1 | 5 |
| β-strand | 1311-1318 | 8 | 2 |
| α-helix | 1323-1330 | 8 | |
| β-strand | 1332 | 1 | 6 |
| α-helix | 1336-1338 | 3 | |
| β-strand | 1343-1345 | 3 | 7 |
| β-strand | 1348-1350 | 3 | 7 |
| β-strand | 1362 | 1 | 6 |
| α-helix | 1367-1371 | 5 | |
| α-helix | 1375-1376 | 2 | |
| β-strand | 1385-1387 | 3 | 8 |
| α-helix | 1395-1401 | 7 | |
| β-strand | 1408-1410 | 3 | 8 |
| α-helix | 1419-1426 | 8 | |
| α-helix | 1436-1438 | 3 | |
| β-strand | 1444-1445 | 2 | 9 |
| β-strand | 1451-1452 | 2 | 9 |
| β-strand | 1453 | 1 | 10 |
| α-helix | 1454-1456 | 3 | |
| β-strand | 1459 | 1 | 11 |
| β-strand | 1474 | 1 | 11 |
| α-helix | 1477-1479 | 3 | |
| α-helix | 1484-1486 | 3 | |
| β-strand | 1494 | 1 | 10 |
| α-helix | 1499-1503 | 5 | |
| α-helix | 1504-1506 | 3 | |
| α-helix | 1508-1510 | 3 | |
| α-helix | 1515 | 1 | |
| β-strand | 1516 | 1 | 12 |
| α-helix | 1517 | 1 | |
| β-strand | 1523 | 1 | 5 |
| α-helix | 1524-1526 | 3 | |
| β-strand | 1540 | 1 | 12 |
| β-strand | 1547 | 1 | 12 |
| α-helix | 1548-1549 | 2 | |
| α-helix | 1550-1556 | 7 | |
| α-helix | 1569-1578 | 10 | |
| α-helix | 1580-1581 | 2 | |
| α-helix | 1582-1607 | 26 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| DNA (cytosine-5)-methyltransferase 1 | A | protein | 1266 | Homo sapiens | P26358 (AlphaFold model) |
| DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3') | B | DNA | 12 | synthetic construct | |
| DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3') | C | DNA | 12 | synthetic construct |
>7XIB_1 DNA (cytosine-5)-methyltransferase 1 (chains A) PKCIQCGQYLDDPDLKYGQHPPDAVDEPQMLTNEKLSIFDANESGFESYEALPQHKLTCF SVYCKHGHLCPIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPINEWWITGFD GGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEFLQSNSDSTYEDLINK IETTVPPSGLNLNRFTEDSLLRHAQFVVEQVESYDEAGDSDEQPIFLTPCMRDLIKLAGV TLGQRRAQARRQTIRHSTREKDRGPTKATTTKLVYQIFDTFFAEQIEKDDREDKENAFKR RRCGVCEVCQQPECGKCKACKDMVKFGGSGRSKQACQERRCPNMAMKEADDDEEVDDNIP EMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDS SKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHS KVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKF KFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNI KLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPN ETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPE CVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSEP EIEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTED CNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVS FLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTR RRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDT MSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPL APGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAAR QFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSV RECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKARESASAKIKE EEAAKD
>7XIB_2 DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3') (chains B) ACTTACGGAAGG
>7XIB_3 DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3') (chains C) CCTTCCGTAAGT
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 2 |
Structural basis for activation of DNMT1. Kikuchi, A., Onoda, H., Yamaguchi, K. et al. Nat Commun (2022) 13:7130-7130. DOI 10.1038/s41467-022-34779-4 · PubMed
Other PDB entries of the same protein (UniProt P26358 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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