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8Y0F	Solution NMR structure of the PTK7-binding DNA aptamer sgc8c Descriptor: DNA Authors: He, A, Wan, L, Guo, P, Han, D. Deposit date: 2024-01-22 Release date: 2024-06-26 Last modified: 2024-07-24 Method: SOLUTION NMR Cite: Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization. Proc.Natl.Acad.Sci.USA, 121, 2024
6ZH2	Cryo-EM structure of DNA-PKcs (State 1) Descriptor: DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-PKcs Authors: Chaplin, A.K, Hardwick, S.W, Chirgadze, D.Y, Blundell, T.L. Deposit date: 2020-06-20 Release date: 2020-10-21 Last modified: 2024-05-01 Method: ELECTRON MICROSCOPY (3.92 Å) Cite: Dimers of DNA-PK create a stage for DNA double-strand break repair. Nat.Struct.Mol.Biol., 28, 2021
6ZHE	Cryo-EM structure of DNA-PK dimer Descriptor: DNA (25-MER), DNA (26-MER), DNA (27-MER), ... Authors: Chaplin, A.K, Hardwick, S.W, Chirgadze, D.Y, Blundell, T.L. Deposit date: 2020-06-23 Release date: 2020-10-21 Last modified: 2024-05-01 Method: ELECTRON MICROSCOPY (7.24 Å) Cite: Dimers of DNA-PK create a stage for DNA double-strand break repair. Nat.Struct.Mol.Biol., 28, 2021
6ZFP	Cryo-EM structure of DNA-PKcs (State 2) Descriptor: DNA-dependent protein kinase catalytic subunit,DNA-PKcs,DNA-PKcs Authors: Chaplin, A.K, Hardwick, S.W, Chirgadze, D.Y, Blundell, T.L. Deposit date: 2020-06-17 Release date: 2020-10-21 Last modified: 2024-05-01 Method: ELECTRON MICROSCOPY (3.24 Å) Cite: Dimers of DNA-PK create a stage for DNA double-strand break repair. Nat.Struct.Mol.Biol., 28, 2021
6ZH4	Cryo-EM structure of DNA-PKcs (State 3) Descriptor: DNA-dependent protein kinase catalytic subunit,DNA-PKcs Authors: Chaplin, A.K, Hardwick, S.W, Chirgadze, D.Y, Blundell, T.L. Deposit date: 2020-06-20 Release date: 2020-10-21 Last modified: 2024-05-01 Method: ELECTRON MICROSCOPY (3.62 Å) Cite: Dimers of DNA-PK create a stage for DNA double-strand break repair. Nat.Struct.Mol.Biol., 28, 2021
6ZH6	Cryo-EM structure of DNA-PKcs:Ku80ct194 Descriptor: DNA-dependent protein kinase catalytic subunit,DNA-PKcs, X-ray repair cross-complementing protein 5 Authors: Chaplin, A.K, Hardwick, S.W, Chirgadze, D.Y, Blundell, T.L. Deposit date: 2020-06-21 Release date: 2020-10-21 Last modified: 2024-05-01 Method: ELECTRON MICROSCOPY (3.93 Å) Cite: Dimers of DNA-PK create a stage for DNA double-strand break repair. Nat.Struct.Mol.Biol., 28, 2021
8ICX	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DTTP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Descriptor: DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3'), MANGANESE (II) ION, ... Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1995-12-15 Release date: 1996-11-15 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (3 Å) Cite: A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta Biochemistry, 35, 1996
5Y3R	Cryo-EM structure of Human DNA-PK Holoenzyme Descriptor: DNA (34-MER), DNA (36-MER), DNA-dependent protein kinase catalytic subunit, ... Authors: Yin, X, Liu, M, Tian, Y, Wang, J, Xu, Y. Deposit date: 2017-07-29 Release date: 2017-09-06 Last modified: 2025-07-02 Method: ELECTRON MICROSCOPY (6.6 Å) Cite: Cryo-EM structure of human DNA-PK holoenzyme Cell Res., 27, 2017
1LAU	URACIL-DNA GLYCOSYLASE Descriptor: DNA (5'-D(*TP*TP*T)-3'), PROTEIN (URACIL-DNA GLYCOSYLASE (E.C.3.2.2.-)) Authors: Pearl, L.H, Savva, R. Deposit date: 1996-01-03 Release date: 1996-06-10 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (1.8 Å) Cite: The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature, 373, 1995
4WKJ	Crystallographic Structure of a Dodecameric RNA-DNA Hybrid Descriptor: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'), MAGNESIUM ION, RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3') Authors: Davis, R.R, Shaban, N.M, Perrino, F.W, Hollis, T. Deposit date: 2014-10-02 Release date: 2014-10-22 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding. Cell Cycle, 14, 2015
8HPA	Monkeypox virus DNA replication holoenzyme F8, A22 and E4 complex in a DNA binding form Descriptor: DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3'), DNA (5'-D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3'), DNA polymerase, ... Authors: Xu, Y, Wu, Y, Zhang, Y, Fan, R, Yang, Y, Li, D, Yang, B, Zhang, Z, Dong, C. Deposit date: 2022-12-12 Release date: 2024-01-31 Last modified: 2025-06-18 Method: ELECTRON MICROSCOPY (3.01 Å) Cite: Cryo-EM structures of human monkeypox viral replication complexes with and without DNA duplex. Cell Res., 33, 2023
5J3I	NMR solution structure of [Sp, Sp]-PT dsDNA Descriptor: DNA (5'-D(*CP*GP*(SSG)P*CP*CP*GP*CP*CP*GP*A)-3'), DNA (5'-D(*TP*CP*GP*GP*CP*GP*(SSG)P*CP*CP*G)-3') Authors: Lan, W, Hu, Z, Cao, C. Deposit date: 2016-03-30 Release date: 2016-11-16 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Structural investigation into physiological DNA phosphorothioate modification Sci Rep, 6, 2016
1KSP	DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex Descriptor: DNA (5'-D(P*TP*TP*PST)-3'), PROTEIN (DNA POLYMERASE I-KLENOW FRAGMENT (E.C.2.7.7.7)), ZINC ION Authors: Brautigam, C.A, Steitz, T.A. Deposit date: 1997-08-19 Release date: 1998-02-25 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J.Mol.Biol., 277, 1998
7RPX	Archaeal DNA ligase and heterotrimeric PCNA in complex with end-joined DNA Descriptor: DNA ligase, DNA polymerase sliding clamp 1, DNA polymerase sliding clamp 2, ... Authors: Sverzhinsky, A, Pascal, J.M. Deposit date: 2021-08-04 Release date: 2021-11-17 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (4.2 Å) Cite: Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure, 30, 2022
1KRP	DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex Descriptor: DNA (5'-D(P*TP*TP*PST)-3'), PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7)), ZINC ION Authors: Brautigam, C.A, Steitz, T.A. Deposit date: 1997-08-19 Release date: 1998-02-25 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J.Mol.Biol., 277, 1998
3JX7	Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-METHYLADENINE analog Descriptor: DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*AP*CP*TP*(DZM)P*AP*CP*GP*GP*G)-3'), alkylpurine DNA glycosylase AlkD Authors: Rubinson, E.H, Eichman, B.F. Deposit date: 2009-09-18 Release date: 2010-09-22 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (1.6 Å) Cite: An unprecedented nucleic acid capture mechanism for excision of DNA damage. Nature, 468, 2010
9BH8	Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology searching conformation Descriptor: DNA polymerase theta, Stem-loop DNA with microhomology in the 3' overhang Authors: Zerio, C.J, Lander, G.C. Deposit date: 2024-04-19 Release date: 2024-05-01 Last modified: 2025-06-25 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: Human polymerase theta helicase positions DNA microhomologies for double-strand break repair. Nat.Struct.Mol.Biol., 32, 2025
9BHA	Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology annealed conformation Descriptor: DNA polymerase theta, Stem-loop DNA with microhomology in the 3' overhang Authors: Zerio, C.J, Lander, G.C. Deposit date: 2024-04-19 Release date: 2024-05-01 Last modified: 2025-06-25 Method: ELECTRON MICROSCOPY (3.5 Å) Cite: Human polymerase theta helicase positions DNA microhomologies for double-strand break repair. Nat.Struct.Mol.Biol., 32, 2025
9BH9	Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology aligning conformation Descriptor: DNA polymerase theta, Stem-loop DNA with microhomology in the 3' overhang Authors: Zerio, C.J, Lander, G.C. Deposit date: 2024-04-19 Release date: 2024-05-01 Last modified: 2025-06-25 Method: ELECTRON MICROSCOPY (3.5 Å) Cite: Human polymerase theta helicase positions DNA microhomologies for double-strand break repair. Nat.Struct.Mol.Biol., 32, 2025
1UGI	URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN Descriptor: IMIDAZOLE, SULFATE ION, URACIL-DNA GLYCOSYLASE INHIBITOR Authors: Putnam, C.D, Arvai, A.S, Mol, C.D, Tainer, J.A. Deposit date: 1998-11-04 Release date: 1999-03-25 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (1.55 Å) Cite: Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase J.Mol.Biol., 287, 1999
8AAS	Crystal structure of the Pyrococcus abyssi RPA trimerization core bound to poly-dT20 ssDNA Descriptor: CALCIUM ION, DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'), RPA14 subunit of the hetero-oligomeric complex involved in homologous recombination, ... Authors: Madru, C, Legrand, P, Sauguet, L. Deposit date: 2022-07-01 Release date: 2023-05-03 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (3.2 Å) Cite: DNA-binding mechanism and evolution of replication protein A. Nat Commun, 14, 2023
9BH7	Human DNA polymerase theta helicase domain dimer in the apo form Descriptor: DNA polymerase theta Authors: Zerio, C.J, Lander, G.C. Deposit date: 2024-04-19 Release date: 2024-05-01 Last modified: 2025-06-25 Method: ELECTRON MICROSCOPY (3.5 Å) Cite: Human polymerase theta helicase positions DNA microhomologies for double-strand break repair. Nat.Struct.Mol.Biol., 32, 2025
9BH6	Human DNA polymerase theta helicase domain tetramer in the apo form Descriptor: DNA polymerase theta Authors: Zerio, C.J, Lander, G.C. Deposit date: 2024-04-19 Release date: 2024-05-01 Last modified: 2025-06-25 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Human polymerase theta helicase positions DNA microhomologies for double-strand break repair. Nat.Struct.Mol.Biol., 32, 2025
6L5B	The structure of the UdgX mutant H109E at a post-excision state Descriptor: IRON/SULFUR CLUSTER, Uracil DNA glycosylase superfamily protein Authors: Xie, W, Tu, J, Zeng, H. Deposit date: 2019-10-22 Release date: 2020-10-28 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.00004983 Å) Cite: Structural insights into an MsmUdgX mutant capable of both crosslinking and uracil excision capability. DNA Repair (Amst), 97, 2021
6L5A	The structure of the UdgX mutant H109E at a pre-excision state Descriptor: GLYCEROL, IRON/SULFUR CLUSTER, Uracil DNA glycosylase superfamily protein Authors: Xie, W, Tu, J, Zeng, H. Deposit date: 2019-10-22 Release date: 2020-10-28 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (1.80007327 Å) Cite: Structural insights into an MsmUdgX mutant capable of both crosslinking and uracil excision capability. DNA Repair (Amst), 97, 2021

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