2DEO
 
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3ABM
 | | Bovine heart cytochrome c oxidase at the fully oxidized state (200-s X-ray exposure dataset) | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S. | | Deposit date: | 2009-12-16 | | Release date: | 2010-01-19 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106, 2009
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2ZXW
 | | Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset) | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Hirata, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S. | | Deposit date: | 2009-01-08 | | Release date: | 2009-02-24 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106, 2009
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3ABL
 | | Bovine heart cytochrome c oxidase at the fully oxidized state (15-s X-ray exposure dataset) | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S. | | Deposit date: | 2009-12-16 | | Release date: | 2010-01-19 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106, 2009
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3O59
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7L7B
 | | Clostridioides difficile RNAP with fidaxomicin | | Descriptor: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | | Authors: | Boyaci, H, Campbell, E.A, Darst, S.A, Chen, J. | | Deposit date: | 2020-12-28 | | Release date: | 2022-02-02 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (3.26 Å) | | Cite: | Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile.
Nature, 604, 2022
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6LBW
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8HU5
 | | Crystal structure of DNA octamer containing GuNA[Me,tBu] | | Descriptor: | DNA (5'-D(*GP*(LR6)P*GP*(BRU)P*AP*CP*AP*C)-3') | | Authors: | Aoyama, H, Obika, H, Yamaguchi, T. | | Deposit date: | 2022-12-22 | | Release date: | 2023-08-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (0.93 Å) | | Cite: | Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
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8HIS
 | | Crystal structure of DNA decamer containing GuNA[Me,tBu] | | Descriptor: | CACODYLIC ACID, DNA (5'-D(*GP*CP*GP*TP*AP*(LR6)P*AP*CP*GP*C)-3') | | Authors: | Aoyama, H, Obika, S, Yamaguchi, T. | | Deposit date: | 2022-11-21 | | Release date: | 2023-08-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
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8I50
 | | Crystal structure of DNA octamer containing GuNA[Me,Me] | | Descriptor: | DNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3') | | Authors: | Aoyama, H, Obika, S, Yamaguchi, T. | | Deposit date: | 2023-01-21 | | Release date: | 2023-08-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (0.95 Å) | | Cite: | Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res., 51, 2023
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7VCG
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3AMO
 | | Time-resolved X-ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase from Arthrobacter globiformis | | Descriptor: | COPPER (II) ION, GLYCEROL, Phenylethylamine oxidase, ... | | Authors: | Kataoka, M, Oya, H, Tominaga, A, Otsu, M, Okajima, T, Tanizawa, K, Yamaguchi, H. | | Deposit date: | 2010-08-20 | | Release date: | 2011-11-23 | | Last modified: | 2017-10-11 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Detection of the reaction intermediates catalyzed by a copper amine oxidase.
J.SYNCHROTRON RADIAT., 18, 2011
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2RU3
 | | Solution structure of c.elegans SUP-12 RRM in complex with RNA | | Descriptor: | Protein SUP-12, isoform a, RNA (5'-R(*GP*UP*GP*UP*GP*C)-3') | | Authors: | Takahashi, M, Kuwasako, K, Unzai, S, Tsuda, K, Yoshikawa, S, He, F, Kobayashi, N, Guntert, P, Shirouzu, M, Ito, T, Tanaka, A, Yokoyama, S, Hagiwara, M, Kuroyanagi, H, Muto, Y. | | Deposit date: | 2013-11-12 | | Release date: | 2014-08-13 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing
Nat.Struct.Mol.Biol., 21, 2014
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1OCC
 | | STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE | | Descriptor: | COPPER (II) ION, CYTOCHROME C OXIDASE, HEME-A, ... | | Authors: | Tsukihara, T, Aoyama, H, Yamashita, E, Tomizaki, T, Yamaguchi, H, Shinzawa-Itoh, K, Nakashima, R, Yaono, R, Yoshikawa, S. | | Deposit date: | 1996-04-18 | | Release date: | 1996-12-07 | | Last modified: | 2018-03-21 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A.
Science, 272, 1996
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1V55
 | | Bovine heart cytochrome c oxidase at the fully reduced state | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Tsukihara, T, Shimokata, K, Katayama, Y, Shimada, H, Muramoto, K, Aoyama, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Yao, M, Ishimura, Y, Yoshikawa, S. | | Deposit date: | 2003-11-21 | | Release date: | 2003-12-23 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
Proc.Natl.Acad.Sci.Usa, 100, 2003
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6VVZ
 | | Mycobacterium tuberculosis RNAP S456L mutant transcription initiation intermediate structure with Sorangicin | | Descriptor: | DNA (62-MER), DNA (65-MER), DNA-directed RNA polymerase subunit alpha, ... | | Authors: | Lilic, M, Boyaci, H, Chen, J, Darst, S.A, Campbell, E.A. | | Deposit date: | 2020-02-18 | | Release date: | 2020-10-21 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.72 Å) | | Cite: | The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.
Proc.Natl.Acad.Sci.USA, 117, 2020
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6VVY
 | | Mycobacterium tuberculosis WT RNAP transcription open promoter complex with Sorangicin | | Descriptor: | DNA (65-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Lilic, M, Boyaci, H, Chen, J, Darst, S.A, Campbell, E.A. | | Deposit date: | 2020-02-18 | | Release date: | 2020-10-21 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.42 Å) | | Cite: | The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.
Proc.Natl.Acad.Sci.USA, 117, 2020
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6VVX
 | | Mycobacterium tuberculosis WT RNAP transcription initiation intermediate structure with Sorangicin | | Descriptor: | DNA (63-MER), DNA (65-MER), DNA-directed RNA polymerase subunit alpha, ... | | Authors: | Lilic, M, Boyaci, H, Chen, J, Campbell, E.A, Darst, S.A. | | Deposit date: | 2020-02-18 | | Release date: | 2020-10-21 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.39 Å) | | Cite: | The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.
Proc.Natl.Acad.Sci.USA, 117, 2020
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6VW0
 | | Mycobacterium tuberculosis RNAP S456L mutant open promoter complex | | Descriptor: | DNA (65-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Lilic, M, Boyaci, H, Chen, J, Darst, S.A, Campbell, E.A. | | Deposit date: | 2020-02-18 | | Release date: | 2020-10-21 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.59 Å) | | Cite: | The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.
Proc.Natl.Acad.Sci.USA, 117, 2020
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2EI9
 | | Crystal structure of R1Bm endonuclease domain | | Descriptor: | ACETIC ACID, Non-LTR retrotransposon R1Bmks ORF2 protein | | Authors: | Maita, N, Aoyagi, H, Osanai, M, Shirakawa, M, Fujiwara, H. | | Deposit date: | 2007-03-12 | | Release date: | 2007-07-17 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies.
Nucleic Acids Res., 35, 2007
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2DYS
 | | Bovine heart cytochrome C oxidase modified by DCCD | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Shinzawa-Itoh, K, Aoyama, H, Muramoto, K, Kurauchi, T, Mizushima, T, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | Deposit date: | 2006-09-16 | | Release date: | 2007-04-03 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase
Embo J., 26, 2007
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2DYR
 | | Bovine heart cytochrome C oxidase at the fully oxidized state | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Shinzawa-Itoh, K, Aoyama, H, Muramoto, K, Kurauchi, T, Mizushima, T, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | Deposit date: | 2006-09-16 | | Release date: | 2007-04-03 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase
Embo J., 26, 2007
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2MGZ
 | | Solution structure of RBFOX family ASD-1 RRM and SUP-12 RRM in ternary complex with RNA | | Descriptor: | Protein ASD-1, isoform a, Protein SUP-12, ... | | Authors: | Takahashi, M, Kuwasako, K, Unzai, S, Tsuda, K, Yoshikawa, S, He, F, Kobayashi, N, Guntert, P, Shirouzu, M, Ito, T, Tanaka, A, Yokoyama, S, Hagiwara, M, Kuroyanagi, H, Muto, Y. | | Deposit date: | 2013-11-12 | | Release date: | 2014-08-13 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing
Nat.Struct.Mol.Biol., 21, 2014
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3NP0
 | | Crystal Structure of Pd(allyl)/apo-E45C/H49A/R52H-rHLFr | | Descriptor: | 1,2-ETHANEDIOL, CADMIUM ION, Ferritin light chain, ... | | Authors: | Wang, Z, Ueno, T, Abe, S, Takezawa, Y, Aoyagi, H, Hikage, T, Watanabe, Y, Kitagawa, S. | | Deposit date: | 2010-06-27 | | Release date: | 2010-12-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | Definite coordination arrangement of organometallic palladium complexes accumulated on the designed interior surface of apo-ferritin.
Chem.Commun.(Camb.), 47, 2011
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3NOZ
 | | Crystal Structure of Pd(allyl)/apo-E45C/R52H-rHLFr | | Descriptor: | 1,2-ETHANEDIOL, CADMIUM ION, Ferritin light chain, ... | | Authors: | Wang, Z, Ueno, T, Abe, S, Takezawa, Y, Aoyagi, H, Hikage, T, Watanabe, Y, Kitagawa, S. | | Deposit date: | 2010-06-27 | | Release date: | 2010-12-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | Definite coordination arrangement of organometallic palladium complexes accumulated on the designed interior surface of apo-ferritin.
Chem.Commun.(Camb.), 47, 2011
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