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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "RPTOR"

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Search Summary

This query matches 19 Structures.

Refinements

Structure Determination Methodology

experimental (19)

Scientific Name of Source Organism

	Homo sapiens (19)
	synthetic construct (1)

Taxonomy

	Eukaryota (19)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (17)
	ELECTRON MICROSCOPY (1)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (19)
	DNA (10)

Refinement Resolution (Å)

	1.5 - 2.0 (3)
	2.0 - 2.5 (7)
	2.5 - 3.0 (6)
	3.0 - 3.5 (1)
	3.5 - 4.0 (1)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (2)
	2015 - 2019 (6)
	2020 - 2024 (9)
	2025 - 2029 (1)

Enzyme Classification Name

	Transferases (19)
	Hydrolases (3)

Symmetry Type

Asymmetric (19)

SCOP Classification

	Alpha and beta proteins (a+b) (2)
	Artifacts (1)
	All beta proteins (1)
	Alpha and beta proteins (a/b) (1)
	Peptides (1)
	Small proteins (1)

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1 to 19 of 19 Structures

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Explore in 3D

3EPZ \| pdb_00003epz	Download File View File

Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1

Walker, J.R., Avvakumov, G.V., Xue, S., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

(2011) J Biological Chem 286: 15344-15351

Released	2008-11-25
Method	X-RAY DIFFRACTION 2.31 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	BGC, GOL, NA, ZN

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3PTA \| pdb_00003pta	Download File View File

Crystal structure of human DNMT1(646-1600) in complex with DNA

Song, J., Patel, D.J.

(2011) Science 331: 1036-1040

Released	2010-12-29
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(CPCPTPGPCPGPGPAPGPGPCPTPCPAPCPGPGPGPA)-3') (nucleic acid) DNA (5'-D(TPCPCPCPGPTPGPAPGPCPCPTPCPCPGPCPAPGPG)-3') (nucleic acid)
Unique Ligands	SAH, ZN

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3SWR \| pdb_00003swr	Download File View File

Structure of human DNMT1 (601-1600) in complex with Sinefungin

Hashimoto, H., Cheng, X.

To be published

Released	2011-08-10
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	EDO, MES, SFG, SO4, ZN

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4WXX \| pdb_00004wxx	Download File View File

The crystal structure of human DNMT1(351-1600)

Zhang, Z.M., Song, J.

(2015) J Mol Biology 427: 2520-2531

Released	2015-07-15
Method	X-RAY DIFFRACTION 2.622 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	SAH, ZN

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4YOC \| pdb_00004yoc	Download File View File

Crystal Structure of human DNMT1 and USP7/HAUSP complex

Cheng, J., Yang, H., Fang, J., Gong, R., Wang, P., Li, Z., Xu, Y.

(2015) Nat Commun 6: 7023-7023

Released	2015-05-27
Method	X-RAY DIFFRACTION 2.916 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)
Unique Ligands	ZN

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4Z96 \| pdb_00004z96	Download File View File

Crystal structure of DNMT1 in complex with USP7

Zhang, Z.M., Song, J.

To be published

Released	2016-10-12
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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4Z97 \| pdb_00004z97	Download File View File

Crystal structure of USP7 in complex with DNMT1(K1115Q)

Zhang, Z.M., Song, J.

To be published

Released	2016-10-12
Method	X-RAY DIFFRACTION 2.998 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)
Unique Ligands	GOL

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5WVO \| pdb_00005wvo	Download File View File

Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3

Ishiyama, S., Nishiyama, A., Nakanishi, M., Arita, K.

(2017) Mol Cell 68: 350-360.e7

Released	2017-11-15
Method	X-RAY DIFFRACTION 1.997 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Histone H3.1 (protein) Ubiquitin (protein)
Unique Ligands	ZN

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5YDR \| pdb_00005ydr	Download File View File

Structure of DNMT1 RFTS domain in complex with ubiquitin

Qian, C.

(2018) Nucleic Acids Res 46: 3218-3231

Released	2018-02-21
Method	X-RAY DIFFRACTION 2.003 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Polyubiquitin-B (protein)
Unique Ligands	PO4, ZN

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6X9I \| pdb_00006x9i	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA

Pathuri, S., Horton, J.R., Cheng, X.

(2021) Nat Cancer 2: 1002-1017

Released	2021-07-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(GPAPGPGPCP(5CM)PGPCPCPTPGPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPG)-R(P(PYO))-D(PGPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, GOL, SAH, ZN

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6X9J \| pdb_00006x9j	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052

Pathuri, S., Horton, J.R., Cheng, X.

(2021) Nat Cancer 2: 1002-1017

Released	2021-07-07
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(GPAPGPGPCP(5CM)PGPCPCPTPGPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPG)-R(P(PYO))-D(PGPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, X52, ZN

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6X9K \| pdb_00006x9k	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A

Pathuri, S., Horton, J.R., Cheng, X.

(2021) Nat Cancer 2: 1002-1017

Released	2021-07-07
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(GPAPGPGPCP(5CM)PGPCPCPTPGPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPG)-R(P(PYO))-D(PGPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, UXM, ZN

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7SFC \| pdb_00007sfc	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A

Horton, J.R., Pathuri, S., Cheng, X.

(2022) Structure 30: 793-802.e5

Released	2022-03-30
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (12-MER) (nucleic acid)
Unique Ligands	EDO, GOL, I67, ZN

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7SFD \| pdb_00007sfd	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A

Horton, J.R., Pathuri, S., Cheng, X.

(2022) Structure 30: 793-802.e5

Released	2022-03-30
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (12-MER) (nucleic acid)
Unique Ligands	EDO, GOL, IO5, SAH, ZN

Explore in 3D

7SFE \| pdb_00007sfe	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830334A

Horton, J.R., Pathuri, S., Cheng, X.

(2022) Structure 30: 793-802.e5

Released	2022-03-30
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (12-MER) (nucleic acid)
Unique Ligands	96I, EDO, GOL, ZN

Explore in 3D

7SFF \| pdb_00007sff	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B

Horton, J.R., Pathuri, S., Cheng, X.

(2022) Structure 30: 793-802.e5

Released	2022-03-30
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (12-MER) (nucleic acid)
Unique Ligands	C79, EDO, GOL, ZN

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7SFG \| pdb_00007sfg	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM

Horton, J.R., Pathuri, S., Cheng, X.

(2022) Structure 30: 793-802.e5

Released	2022-03-30
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA Strand 1 (nucleic acid) DNA Strand 2 (nucleic acid)
Unique Ligands	EDO, GOL, SAM, ZN

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8V9U \| pdb_00008v9u	Download File View File

Solution NMR structure of human DNMT1 N-terminal alpha-helical domain

Hu, Q., Botuyan, M.V., Mer, G.

(2024) J Biological Chem 300: 105775-105775

Released	2024-02-28
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)

Explore in 3D

8XQC \| pdb_00008xqc	Download File View File

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog

Kikuchi, A., Hayashi, G., Kori, S., Arita, K.

To be published

Released	2025-01-15
Method	ELECTRON MICROSCOPY 3.25 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(APCPTPTPAP(5CM)PGPGPAPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPTPCP(C55)PGPTPAPAPGPT)-3') (nucleic acid)
Unique Ligands	SAH, ZN

1 to 19 of 19 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

3EPZ | pdb_00003epz

Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1

3PTA | pdb_00003pta

Crystal structure of human DNMT1(646-1600) in complex with DNA

3SWR | pdb_00003swr

Structure of human DNMT1 (601-1600) in complex with Sinefungin

4WXX | pdb_00004wxx

The crystal structure of human DNMT1(351-1600)

4YOC | pdb_00004yoc

Crystal Structure of human DNMT1 and USP7/HAUSP complex

4Z96 | pdb_00004z96

Crystal structure of DNMT1 in complex with USP7

4Z97 | pdb_00004z97

Crystal structure of USP7 in complex with DNMT1(K1115Q)

5WVO | pdb_00005wvo

Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3

5YDR | pdb_00005ydr

Structure of DNMT1 RFTS domain in complex with ubiquitin

6X9I | pdb_00006x9i

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA

6X9J | pdb_00006x9j

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052

6X9K | pdb_00006x9k

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A

7SFC | pdb_00007sfc

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A

7SFD | pdb_00007sfd

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A

7SFE | pdb_00007sfe

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830334A

7SFF | pdb_00007sff

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B

7SFG | pdb_00007sfg

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM

8V9U | pdb_00008v9u

Solution NMR structure of human DNMT1 N-terminal alpha-helical domain

8XQC | pdb_00008xqc

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

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Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

3EPZ | pdb_00003epz

3PTA | pdb_00003pta

3SWR | pdb_00003swr

4WXX | pdb_00004wxx

4YOC | pdb_00004yoc

4Z96 | pdb_00004z96

4Z97 | pdb_00004z97

5WVO | pdb_00005wvo

5YDR | pdb_00005ydr

6X9I | pdb_00006x9i

6X9J | pdb_00006x9j

6X9K | pdb_00006x9k

7SFC | pdb_00007sfc

7SFD | pdb_00007sfd

7SFE | pdb_00007sfe

7SFF | pdb_00007sff

7SFG | pdb_00007sfg

8V9U | pdb_00008v9u

8XQC | pdb_00008xqc