4WXX: Human DNMT1(351-1600)

Name: PDB 4WXX: The crystal structure of human DNMT1(351-1600)
Published: 2015-07-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

The crystal structure of human DNMT1(351-1600). Determined by X-ray diffraction at 2.62 Å resolution. Released 15 Jul 2015.

Method: X-ray diffraction
Resolution: 2.62 Å
Organism: Homo sapiens
Chains: 2
Atoms: 19,035
Mol. weight: 285.63 kDa
Ligands: ZN, SAH
Released: 15 Jul 2015

Explore 4WXX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WXX contains 132 α-helices and 137 β-strands across 2 chains. 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.

Chain A: 64 helices, 70 β-strands

Element	Residues	Length	Sheet
β-strand	352	1	1
β-strand	359	1	1
β-strand	367	1	2
β-strand	374-375	2	3
β-strand	404-409	6	3
β-strand	410	1	4
β-strand	411-413	3	3
β-strand	418	1	2
β-strand	419	1	3
β-strand	434-440	7	3
β-strand	453-458	6	3
β-strand	464-469	6	3
β-strand	475-480	6	3
β-strand	485-488	4	3
α-helix	490	1
β-strand	491	1	4
α-helix	492	1
α-helix	496-518	23
α-helix	524-533	10
α-helix	535-537	3
α-helix	547-552	6
α-helix	554-567	14
α-helix	573-574	2
α-helix	575-577	3
α-helix	579-587	9
α-helix	590-592	3
α-helix	622-634	13
α-helix	662-663	2
α-helix	668-671	4
α-helix	684-686	3
α-helix	692-703	12
α-helix	714-717	4
β-strand	723	1	5
α-helix	724-726	3
β-strand	732-734	3	6
β-strand	739-740	2	7
β-strand	746-748	3	7
β-strand	750-752	3	6
β-strand	756-758	3	6
β-strand	762-765	4	7
β-strand	767	1	5
β-strand	775-784	10	7
β-strand	790-799	10	7
α-helix	800-802	3
α-helix	806-808	3
β-strand	813-824	12	7
α-helix	825-827	3
β-strand	828-832	5	7
β-strand	834-836	3	7
α-helix	838-840	3
α-helix	843-845	3
β-strand	863-870	8	7
β-strand	875-877	3	7
α-helix	878-880	3
α-helix	894-905	12
β-strand	909-910	2	8
β-strand	913-916	4	9
β-strand	920-923	4	9
β-strand	925-928	4	8
β-strand	931-934	4	8
β-strand	938-941	4	9
α-helix	962-964	3
α-helix	972-975	4
α-helix	989-991	3
β-strand	992-1002	11	9
β-strand	1003	1	10
β-strand	1009	1	10
β-strand	1015-1022	8	9
α-helix	1031-1034	4
β-strand	1041-1052	12	9
α-helix	1053-1055	3
β-strand	1058-1064	7	9
α-helix	1072-1076	5
β-strand	1082-1090	9	9
β-strand	1095-1097	3	9
α-helix	1098-1100	3
α-helix	1101-1103	3
α-helix	1136-1138	3
β-strand	1139-1144	6	7
α-helix	1150-1158	9
β-strand	1161-1167	7	7
α-helix	1171-1180	10
β-strand	1185-1187	3	7
α-helix	1191-1198	8
β-strand	1204	1	11
β-strand	1210	1	11
β-strand	1219-1222	4	7
α-helix	1234-1235	2
α-helix	1237-1244	8
α-helix	1247-1258	12
β-strand	1262-1268	7	7
α-helix	1269-1272	4
α-helix	1274-1290	17
β-strand	1293-1300	8	7
α-helix	1301-1304	4
β-strand	1308	1	12
β-strand	1311-1318	8	7
β-strand	1320	1	13
β-strand	1322	1	13
α-helix	1325-1330	6
β-strand	1332	1	14
α-helix	1336-1338	3
β-strand	1343-1345	3	15
β-strand	1348-1350	3	15
β-strand	1362	1	14
α-helix	1363-1365	3
α-helix	1367-1371	5
α-helix	1375-1376	2
β-strand	1385-1386	2	16
α-helix	1395-1401	7
β-strand	1409-1410	2	16
α-helix	1419-1426	8
α-helix	1436-1438	3
β-strand	1444-1445	2	17
β-strand	1451-1452	2	17
α-helix	1453-1457	5
β-strand	1459	1	18
β-strand	1474	1	18
α-helix	1477-1479	3
α-helix	1483-1486	4
α-helix	1499-1503	5
α-helix	1504-1506	3
α-helix	1508-1510	3
α-helix	1515	1
β-strand	1516	1	19
α-helix	1517-1518	2
β-strand	1523	1	12
β-strand	1540	1	19
β-strand	1547	1	19
α-helix	1548-1549	2
α-helix	1550-1556	7
α-helix	1569-1578	10
α-helix	1580-1581	2
α-helix	1582-1601	20

Chain B: 68 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	352	1	20
α-helix	358	1
β-strand	359	1	20
β-strand	367	1	21
α-helix	383-386	4
β-strand	404-409	6	22
β-strand	410	1	23
β-strand	411-413	3	22
β-strand	418	1	21
β-strand	419	1	22
β-strand	434-441	8	22
β-strand	453-458	6	22
β-strand	463-469	7	22
β-strand	475-480	6	22
β-strand	485-488	4	22
β-strand	491	1	23
α-helix	496-518	23
α-helix	524-532	9
α-helix	535-537	3
α-helix	547-552	6
α-helix	554-559	6
α-helix	564-567	4
α-helix	573-574	2
α-helix	575-577	3
α-helix	579-587	9
α-helix	590-592	3
α-helix	616-619	4
α-helix	622-633	12
α-helix	662-663	2
α-helix	668-671	4
α-helix	684-686	3
α-helix	692-702	11
β-strand	723	1	24
α-helix	724-726	3
β-strand	732-734	3	25
β-strand	739-740	2	26
β-strand	746-748	3	26
β-strand	750-752	3	25
β-strand	756-758	3	25
β-strand	762-765	4	26
β-strand	767	1	24
β-strand	775-784	10	26
β-strand	790-799	10	26
α-helix	800-802	3
α-helix	806-808	3
β-strand	813-824	12	26
α-helix	825-827	3
β-strand	830-832	3	26
β-strand	834-836	3	26
α-helix	838-840	3
α-helix	843-845	3
β-strand	863-870	8	26
β-strand	875-877	3	26
α-helix	878-880	3
α-helix	894-905	12
β-strand	909-910	2	27
β-strand	913-916	4	28
β-strand	920-923	4	28
β-strand	925-928	4	27
β-strand	931-934	4	27
β-strand	938-941	4	28
α-helix	961-963	3
α-helix	972-975	4
α-helix	987-991	5
β-strand	992-1002	11	28
β-strand	1003	1	29
β-strand	1009	1	29
α-helix	1010	1
β-strand	1015-1022	8	28
α-helix	1031-1033	3
β-strand	1041-1052	12	28
α-helix	1053-1055	3
β-strand	1058-1064	7	28
α-helix	1065-1067	3
α-helix	1072-1077	6
β-strand	1082-1090	9	28
β-strand	1095-1097	3	28
α-helix	1098-1100	3
α-helix	1101-1103	3
α-helix	1137-1138	2
β-strand	1139-1144	6	26
α-helix	1150-1158	9
β-strand	1161-1167	7	26
α-helix	1171-1180	10
β-strand	1185-1187	3	26
α-helix	1191-1198	8
β-strand	1204	1	30
α-helix	1209	1
β-strand	1210	1	30
α-helix	1211-1212	2
β-strand	1219-1222	4	26
α-helix	1234-1235	2
α-helix	1237-1244	8
α-helix	1247-1258	12
β-strand	1262-1268	7	26
α-helix	1269-1272	4
α-helix	1274-1290	17
β-strand	1293-1300	8	26
α-helix	1301-1304	4
β-strand	1308	1	31
β-strand	1311-1318	8	26
α-helix	1325-1330	6
β-strand	1332	1	32
α-helix	1336-1338	3
β-strand	1343-1345	3	33
β-strand	1348-1350	3	33
β-strand	1362	1	32
α-helix	1363-1365	3
α-helix	1367-1371	5
α-helix	1375-1376	2
β-strand	1385-1386	2	34
α-helix	1395-1401	7
β-strand	1409-1410	2	34
α-helix	1419-1426	8
α-helix	1436-1438	3
β-strand	1444-1445	2	35
β-strand	1451-1452	2	35
α-helix	1453-1457	5
β-strand	1459	1	36
β-strand	1474	1	36
α-helix	1477-1479	3
α-helix	1499-1503	5
α-helix	1504-1506	3
α-helix	1508-1510	3
α-helix	1515	1
β-strand	1516	1	37
α-helix	1517-1518	2
β-strand	1523	1	31
β-strand	1540	1	37
β-strand	1547	1	37
α-helix	1548-1549	2
α-helix	1550-1556	7
α-helix	1569-1578	10
α-helix	1580-1581	2
α-helix	1582-1601	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 1	A, B	protein	1256	Homo sapiens	P26358 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4WXX_1 DNA (cytosine-5)-methyltransferase 1 (chains A, B)
SPKCIQCGQYLDDPDLKYGQHPPDAVDEPQMLTNEKLSIFDANESGFESYEALPQHKLTC
FSVYCKHGHLCPIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPINEWWITGF
DGGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEFLQSNSDSTYEDLIN
KIETTVPPSGLNLNRFTEDSLLRHAQFVVEQVESYDEAGDSDEQPIFLTPCMRDLIKLAG
VTLGQRRAQARRQTIRHSTREKDRGPTKATTTKLVYQIFDTFFAEQIEKDDREDKENAFK
RRRCGVCEVCQQPECGKCKACKDMVKFGGSGRSKQACQERRCPNMAMKEADDDEEVDDNI
PEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDD
SSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIH
SKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNK
FKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFN
IKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRP
NETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLP
ECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSE
PEIEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTE
DCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVV
SFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQT
RRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRD
TMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIP
LAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAA
RQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVS
VRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKALTRVW

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	10
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Primary citation

Crystal Structure of Human DNA Methyltransferase 1. Zhang, Z.M., Liu, S., Lin, K. et al. J Mol Biol (2015) 427:2520-2531. DOI 10.1016/j.jmb.2015.06.001 · PubMed

Other PDB entries of the same protein (UniProt P26358 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6X9J 1.79 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052
6L1F 1.9 Å, Crystal structure of PHF20L1 Tudor1 in complex with K142me1 DNMT1
7SFC 1.97 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A
5WVO 2.0 Å, Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated…
5YDR 2.0 Å, Structure of DNMT1 RFTS domain in complex with ubiquitin
7SFF 2.05 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B
7SFD 2.09 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A
6X9I 2.2 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA
7XIB 2.23 Å, Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and…
6K3A 2.3 Å, Crystal structure of human PCNA in complex with DNMT1 PIP box motif.
3EPZ 2.31 Å, Structure of the replication foci-targeting sequence of human DNA cytosine…
7SFG 2.43 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM

Browse structure collections

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