3VXN
 
 | | HLA-A24 in complex with HIV-1 Nef134-10(wt) | | Descriptor: | 10-mer peptide from Protein Nef, Beta-2-microglobulin, HLA class I histocompatibility antigen, ... | | Authors: | Shimizu, A, Fukai, S, Yamagata, A, Iwamoto, A. | | Deposit date: | 2012-09-20 | | Release date: | 2013-10-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection
SCI REP, 3, 2013
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3VXO
 | | HLA-A24 in complex with HIV-1 Nef134-10(2F) | | Descriptor: | 10-mer peptide from Protein Nef, Beta-2-microglobulin, HLA class I histocompatibility antigen, ... | | Authors: | Shimizu, A, Fukai, S, Yamagata, A, Iwamoto, A. | | Deposit date: | 2012-09-20 | | Release date: | 2013-10-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.61 Å) | | Cite: | Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection
SCI REP, 3, 2013
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3VXU
 | | The complex between T36-5 TCR and HLA-A24 bound to HIV-1 Nef134-10(2F) peptide | | Descriptor: | 10-mer peptide from Protein Nef, Beta-2-microglobulin, HLA class I histocompatibility antigen, ... | | Authors: | Shimizu, A, Fukai, S, Yamagata, A, Iwamoto, A. | | Deposit date: | 2012-09-20 | | Release date: | 2013-10-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection
SCI REP, 3, 2013
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3VXM
 | | The complex between C1-28 TCR and HLA-A24 bound to HIV-1 Nef134-10(2F) peptide | | Descriptor: | 10-mer peptide from Protein Nef, Beta-2-microglobulin, C1-28 TCR alpha chain, ... | | Authors: | Shimizu, A, Fukai, S, Yamagata, A, Iwamoto, A. | | Deposit date: | 2012-09-20 | | Release date: | 2013-10-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection
SCI REP, 3, 2013
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3VXQ
 | | H27-14 TCR specific for HLA-A24-Nef134-10 | | Descriptor: | H27-14 TCR alpha chain, H27-14 TCR beta chain | | Authors: | Shimizu, A, Fukai, S, Yamagata, A, Iwamoto, A. | | Deposit date: | 2012-09-20 | | Release date: | 2013-10-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection
SCI REP, 3, 2013
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7XI9
 | | Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form) | | Descriptor: | DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3'), DNA (cytosine-5)-methyltransferase 1, ... | | Authors: | Onoda, H, Kikuchi, A, Kori, S, Yoshimi, S, Yamagata, A, Arita, K. | | Deposit date: | 2022-04-12 | | Release date: | 2022-11-30 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (2.52 Å) | | Cite: | Structural basis for activation of DNMT1.
Nat Commun, 13, 2022
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7XIB
 | | Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form) | | Descriptor: | DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3'), DNA (cytosine-5)-methyltransferase 1, ... | | Authors: | Onoda, H, Kikuchi, A, Kori, S, Yoshimi, S, Yamagata, A, Arita, K. | | Deposit date: | 2022-04-12 | | Release date: | 2022-11-30 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (2.23 Å) | | Cite: | Structural basis for activation of DNMT1.
Nat Commun, 13, 2022
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3WLB
 | | HLA-A24 in complex with HIV-1 Nef126-10(8T10F) | | Descriptor: | Beta-2-microglobulin, HLA class I histocompatibility antigen, A-24 alpha chain, ... | | Authors: | Shimizu, A, Fukai, S, Yamagata, A, Iwamoto, A, Han, C. | | Deposit date: | 2013-11-08 | | Release date: | 2014-06-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Switching and emergence of CTL epitopes in HIV-1 infection
Retrovirology, 11, 2014
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3WL9
 | | HLA-A24 in complex with HIV-1 Nef126-10(8I10F) | | Descriptor: | Beta-2-microglobulin, HLA class I histocompatibility antigen, A-24 alpha chain, ... | | Authors: | Shimizu, A, Fukai, S, Yamagata, A, Iwamoto, A, Han, C. | | Deposit date: | 2013-11-08 | | Release date: | 2014-06-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.66 Å) | | Cite: | Switching and emergence of CTL epitopes in HIV-1 infection
Retrovirology, 11, 2014
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5B86
 | | Crystal structure of M-Sec | | Descriptor: | Tumor necrosis factor alpha-induced protein 2 | | Authors: | Yamashita, M, Sato, Y, Yamagata, A, Fukai, S. | | Deposit date: | 2016-06-12 | | Release date: | 2016-10-12 | | Last modified: | 2020-02-26 | | Method: | X-RAY DIFFRACTION (3.017 Å) | | Cite: | Distinct Roles for the N- and C-terminal Regions of M-Sec in Plasma Membrane Deformation during Tunneling Nanotube Formation.
Sci Rep, 6, 2016
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6IXF
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6IXE
 | | Crystal structure of SeMet apo SH3BP5 (I41) | | Descriptor: | SH3 domain-binding protein 5, SUCCINIC ACID | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | | Deposit date: | 2018-12-10 | | Release date: | 2019-03-20 | | Last modified: | 2019-03-27 | | Method: | X-RAY DIFFRACTION (3.35 Å) | | Cite: | Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5.
Life Sci Alliance, 2, 2019
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6IXV
 | | Crystal structure of SH3BP5-Rab11a | | Descriptor: | PHOSPHATE ION, Ras-related protein Rab-11A, SH3 domain-binding protein 5 | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | | Deposit date: | 2018-12-12 | | Release date: | 2019-03-20 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (3.8 Å) | | Cite: | Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5.
Life Sci Alliance, 2, 2019
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6IXG
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7VNY
 | | Rba sphaeroides WT RC-LH1 monomer | | Descriptor: | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE, BACTERIOCHLOROPHYLL A, BACTERIOPHEOPHYTIN B, ... | | Authors: | Bracun, L, Yamagata, A, Liu, L.N, Shirouzu, M. | | Deposit date: | 2021-10-12 | | Release date: | 2022-06-01 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (2.79 Å) | | Cite: | Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.
Nat Commun, 13, 2022
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7VB9
 | | Rba sphaeroides PufY-KO RC-LH1 dimer type-2 | | Descriptor: | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE, BACTERIOCHLOROPHYLL A, BACTERIOPHEOPHYTIN A, ... | | Authors: | Bracun, L, Yamagata, A, Liu, L.N, Shirouzu, M. | | Deposit date: | 2021-08-30 | | Release date: | 2022-05-04 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (3.45 Å) | | Cite: | Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.
Nat Commun, 13, 2022
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7VOY
 | | Rba sphaeroides PufX-KO RC-LH1 | | Descriptor: | BACTERIOCHLOROPHYLL A, BACTERIOPHEOPHYTIN A, FE (II) ION, ... | | Authors: | Bracun, L, Yamagata, A, Liu, L.N, Shirouzu, M. | | Deposit date: | 2021-10-15 | | Release date: | 2022-05-04 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (4.2 Å) | | Cite: | Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.
Nat Commun, 13, 2022
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7VA9
 | | Rba sphaeroides PufY-KO RC-LH1 dimer type-1 | | Descriptor: | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE, BACTERIOCHLOROPHYLL A, BACTERIOPHEOPHYTIN B, ... | | Authors: | Bracun, L, Yamagata, A, Liu, L.N, Shirouzu, M. | | Deposit date: | 2021-08-27 | | Release date: | 2022-05-04 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (3.08 Å) | | Cite: | Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.
Nat Commun, 13, 2022
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7VNM
 | | Rba sphaeroides PufY-KO RC-LH1 monomer | | Descriptor: | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE, BACTERIOCHLOROPHYLL A, BACTERIOPHEOPHYTIN A, ... | | Authors: | Bracun, L, Yamagata, A, Liu, L.N, Shirouzu, M. | | Deposit date: | 2021-10-11 | | Release date: | 2022-05-04 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (2.86 Å) | | Cite: | Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.
Nat Commun, 13, 2022
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3VLC
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3A58
 | | Crystal structure of Sec3p - Rho1p complex from Saccharomyces cerevisiae | | Descriptor: | Exocyst complex component SEC3, GTP-binding protein RHO1, MAGNESIUM ION, ... | | Authors: | Yamashita, M, Sato, Y, Yamagata, A, Mimura, H, Yoshikawa, A, Fukai, S. | | Deposit date: | 2009-08-03 | | Release date: | 2010-01-12 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis for the Rho- and phosphoinositide-dependent localization of the exocyst subunit Sec3
Nat.Struct.Mol.Biol., 17, 2010
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3A9J
 | | Crystal structure of the mouse TAB2-NZF in complex with Lys63-linked di-ubiquitin | | Descriptor: | Mitogen-activated protein kinase kinase kinase 7-interacting protein 2, Ubiquitin, ZINC ION | | Authors: | Sato, Y, Yoshikawa, A, Yamashita, M, Yamagata, A, Fukai, S. | | Deposit date: | 2009-10-29 | | Release date: | 2009-12-08 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (1.18 Å) | | Cite: | Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3
Embo J., 28, 2009
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3A9K
 | | Crystal structure of the mouse TAB3-NZF in complex with Lys63-linked di-ubiquitin | | Descriptor: | Mitogen-activated protein kinase kinase kinase 7-interacting protein 3, Ubiquitin, ZINC ION | | Authors: | Sato, Y, Yoshikawa, A, Yamashita, M, Yamagata, A, Fukai, S. | | Deposit date: | 2009-10-29 | | Release date: | 2009-12-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3
Embo J., 28, 2009
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3B08
 | | Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin | | Descriptor: | Polyubiquitin-C, RanBP-type and C3HC4-type zinc finger-containing protein 1, ZINC ION, ... | | Authors: | Sato, Y, Fujita, H, Yoshikawa, A, Yamashita, M, Yamagata, A, Kaiser, S.E, Iwai, K, Fukai, S. | | Deposit date: | 2011-06-07 | | Release date: | 2011-12-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.701 Å) | | Cite: | Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex
Proc.Natl.Acad.Sci.USA, 108, 2011
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3B0A
 | | Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin | | Descriptor: | Polyubiquitin-C, RanBP-type and C3HC4-type zinc finger-containing protein 1, TRIS(HYDROXYETHYL)AMINOMETHANE, ... | | Authors: | Sato, Y, Fujita, H, Yoshikawa, A, Yamashita, M, Yamagata, A, Kaiser, S.E, Iwai, K, Fukai, S. | | Deposit date: | 2011-06-07 | | Release date: | 2011-12-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex
Proc.Natl.Acad.Sci.USA, 108, 2011
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