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9C0O	Crystal structure of DmCfp1 PHD finger bound to H3K4me3 Descriptor: CXXC-type zinc finger protein 1, DIMETHYL SULFOXIDE, Histone H3.3C, ... Authors: Gregoire, S, Couture, J.F. Deposit date: 2024-05-27 Release date: 2024-07-03 Last modified: 2024-09-18 Method: X-RAY DIFFRACTION (1.53 Å) Cite: Structural insights into an atypical histone binding mechanism by a PHD finger. Structure, 32, 2024
9ATN	NMR structure of the MLL4 PHD2/3 fingers in complex with ASXL2 Descriptor: Histone-lysine N-methyltransferase 2D, Polycomb group protein ASXL2, ZINC ION Authors: Zhang, Y, Zandian, M, Kutateladze, T. Deposit date: 2024-02-27 Release date: 2024-06-19 Method: SOLUTION NMR Cite: ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers. Nat Commun, 15, 2024
8WMS	Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain Descriptor: Developmental pluripotency-associated protein 3, E3 ubiquitin-protein ligase UHRF1, ZINC ION Authors: Shiraishi, N, Arita, K. Deposit date: 2023-10-04 Release date: 2024-07-31 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain To Be Published
8WAR	Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Descriptor: Alpha-amanitin, CDK-activating kinase assembly factor MAT1, DNA-directed RNA polymerase II subunit E, ... Authors: Chen, X, Liu, W, Wang, Q, Wang, X, Ren, Y, Qu, X, Li, W, Xu, Y. Deposit date: 2023-09-08 Release date: 2023-12-06 Last modified: 2024-01-03 Method: ELECTRON MICROSCOPY (7.2 Å) Cite: Structural visualization of transcription initiation in action. Science, 382, 2023
8WAP	Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Descriptor: Alpha-amanitin, CDK-activating kinase assembly factor MAT1, DNA-directed RNA polymerase II subunit E, ... Authors: Chen, X, Liu, W, Wang, Q, Wang, X, Ren, Y, Qu, X, Li, W, Xu, Y. Deposit date: 2023-09-08 Release date: 2023-12-06 Last modified: 2024-01-03 Method: ELECTRON MICROSCOPY (5.85 Å) Cite: Structural visualization of transcription initiation in action. Science, 382, 2023
8WAS	Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Descriptor: Alpha-amanitin, CDK-activating kinase assembly factor MAT1, DNA-directed RNA polymerase II subunit E, ... Authors: Chen, X, Liu, W, Wang, Q, Wang, X, Ren, Y, Qu, X, Li, W, Xu, Y. Deposit date: 2023-09-08 Release date: 2023-12-06 Last modified: 2024-01-03 Method: ELECTRON MICROSCOPY (6.13 Å) Cite: Structural visualization of transcription initiation in action. Science, 382, 2023
8WAQ	Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Descriptor: Alpha-amanitin, CDK-activating kinase assembly factor MAT1, DNA-directed RNA polymerase II subunit E, ... Authors: Chen, X, Liu, W, Wang, Q, Wang, X, Ren, Y, Qu, X, Li, W, Xu, Y. Deposit date: 2023-09-08 Release date: 2023-12-06 Last modified: 2024-01-03 Method: ELECTRON MICROSCOPY (6.29 Å) Cite: Structural visualization of transcription initiation in action. Science, 382, 2023
8WAK	Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Descriptor: Alpha-amanitin, CDK-activating kinase assembly factor MAT1, DNA-directed RNA polymerase II subunit E, ... Authors: Chen, X, Liu, W, Wang, Q, Wang, X, Ren, Y, Qu, X, Li, W, Xu, Y. Deposit date: 2023-09-07 Release date: 2023-12-06 Last modified: 2024-01-03 Method: ELECTRON MICROSCOPY (5.47 Å) Cite: Structural visualization of transcription initiation in action. Science, 382, 2023
8WAN	Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Descriptor: Alpha-amanitin, CDK-activating kinase assembly factor MAT1, DNA-directed RNA polymerase II subunit E, ... Authors: Chen, X, Liu, W, Wang, Q, Wang, X, Ren, Y, Qu, X, Li, W, Xu, Y. Deposit date: 2023-09-07 Release date: 2023-12-06 Last modified: 2024-01-03 Method: ELECTRON MICROSCOPY (6.07 Å) Cite: Structural visualization of transcription initiation in action. Science, 382, 2023
8WAL	Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Descriptor: Alpha-amanitin, CDK-activating kinase assembly factor MAT1, DNA-directed RNA polymerase II subunit E, ... Authors: Chen, X, Liu, W, Wang, Q, Wang, X, Ren, Y, Qu, X, Li, W, Xu, Y. Deposit date: 2023-09-07 Release date: 2023-12-06 Last modified: 2024-01-03 Method: ELECTRON MICROSCOPY (8.52 Å) Cite: Structural visualization of transcription initiation in action. Science, 382, 2023
8WAO	Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Descriptor: Alpha-amanitin, CDK-activating kinase assembly factor MAT1, DNA-directed RNA polymerase II subunit E, ... Authors: Chen, X, Liu, W, Wang, Q, Wang, X, Ren, Y, Qu, X, Li, W, Xu, Y. Deposit date: 2023-09-07 Release date: 2023-12-06 Last modified: 2024-01-03 Method: ELECTRON MICROSCOPY (6.4 Å) Cite: Structural visualization of transcription initiation in action. Science, 382, 2023
8W9F	Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Descriptor: 3-DNA, 5-DNA, Chromatin modification-related protein EAF3, ... Authors: Wang, C, Zhan, X. Deposit date: 2023-09-05 Release date: 2024-05-15 Method: ELECTRON MICROSCOPY (4.4 Å) Cite: Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv, 10, 2024
8W9E	Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Descriptor: 3-DNA, 5-DNA, Chromatin modification-related protein EAF3, ... Authors: Wang, C, Zhan, X. Deposit date: 2023-09-05 Release date: 2024-05-15 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv, 10, 2024
8W9C	Cryo-EM structure of the Rpd3S complex from budding yeast Descriptor: Chromatin modification-related protein EAF3, Histone deacetylase RPD3, POTASSIUM ION, ... Authors: Wang, C, Zhan, X. Deposit date: 2023-09-05 Release date: 2024-05-15 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv, 10, 2024
8W9D	Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Descriptor: 3-DNA, 5-DNA, Chromatin modification-related protein EAF3, ... Authors: Wang, C, Zhan, X. Deposit date: 2023-09-05 Release date: 2024-05-15 Method: ELECTRON MICROSCOPY (3.9 Å) Cite: Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv, 10, 2024
8KD5	Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Descriptor: 187bp DNA, Chromatin modification-related protein EAF3, Histone H2A, ... Authors: Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Chang, X, Chao, W.C.H, He, J. Deposit date: 2023-08-09 Release date: 2023-09-13 Last modified: 2023-10-11 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
8KD3	Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Descriptor: 187bp DNA, Chromatin modification-related protein EAF3, Histone H2A, ... Authors: Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Zhang, X, Chao, W.C.H, He, J. Deposit date: 2023-08-09 Release date: 2023-09-13 Last modified: 2023-10-11 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
8KD6	Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Descriptor: 187bp DNA, Chromatin modification-related protein EAF3, Histone H2A, ... Authors: Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Zhang, X, Chao, W.C.H, He, J. Deposit date: 2023-08-09 Release date: 2023-09-13 Last modified: 2023-10-11 Method: ELECTRON MICROSCOPY (3.07 Å) Cite: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
8KD4	Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Descriptor: 187bp DNA, Chromatin modification-related protein EAF3, Histone H2A, ... Authors: Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Zhang, X, Chao, W.C.H, He, J. Deposit date: 2023-08-09 Release date: 2023-09-13 Last modified: 2023-10-11 Method: ELECTRON MICROSCOPY (2.93 Å) Cite: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
8KD2	Rpd3S in complex with 187bp nucleosome Descriptor: 187bp DNA, Chromatin modification-related protein EAF3, Histone H2A, ... Authors: Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Zhang, X, Chao, W.C.H, He, J. Deposit date: 2023-08-09 Release date: 2023-09-13 Last modified: 2023-10-11 Method: ELECTRON MICROSCOPY (3.02 Å) Cite: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
8KD7	Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Descriptor: 167bp DNA, Chromatin modification-related protein EAF3, Histone H2A, ... Authors: Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Chang, X, Chao, W.C.H, He, J. Deposit date: 2023-08-09 Release date: 2023-09-13 Last modified: 2023-10-11 Method: ELECTRON MICROSCOPY (3.09 Å) Cite: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
8KC7	Rpd3S histone deacetylase complex Descriptor: Chromatin modification-related protein EAF3, Histone deacetylase RPD3, Transcriptional regulatory protein RCO1, ... Authors: Dong, S, Li, H, Wang, M, Rasheed, N, Zou, B, Gao, X, Guan, J, Li, W, Zhang, J, Wang, C, Zhou, N, Shi, X, Li, M, Zhou, M, Huang, J, Li, H, Zhang, Y, Wong, K.H, Zhang, X, Chao, W.C.H, He, J. Deposit date: 2023-08-06 Release date: 2023-09-13 Last modified: 2023-10-18 Method: ELECTRON MICROSCOPY (3.46 Å) Cite: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res., 33, 2023
8TOF	Rpd3S bound to an H3K36Cme3 modified nucleosome Descriptor: Chromatin modification-related protein EAF3, DNA (176-MER), Histone H2A, ... Authors: Markert, J.W, Vos, S.M, Farnung, L. Deposit date: 2023-08-03 Release date: 2024-01-17 Method: ELECTRON MICROSCOPY (2.8 Å) Cite: Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex. Nat Commun, 14, 2023
8JHO	Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Descriptor: Chromatin modification-related protein EAF3, Di-nucleosome template foward, Di-nucleosome template reverse, ... Authors: Wang, H. Deposit date: 2023-05-25 Release date: 2023-09-27 Last modified: 2023-12-27 Method: ELECTRON MICROSCOPY (7.6 Å) Cite: Structure of histone deacetylase complex Rpd3S bound to nucleosome. Nat.Struct.Mol.Biol., 30, 2023
8IHN	Cryo-EM structure of the Rpd3S core complex Descriptor: CALCIUM ION, Chromatin modification-related protein EAF3, Histone H3, ... Authors: Zhang, Y, Gang, C. Deposit date: 2023-02-23 Release date: 2024-03-20 Method: ELECTRON MICROSCOPY (3.37 Å) Cite: Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme. Cell Res., 33, 2023

 

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