Author results

3EA6
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ATOMIC RESOLUTION OF CRYSTAL STRUCTURE OF SEK
Descriptor:Staphylococcal enterotoxin K, ZINC ION, IODIDE ION
Authors:Shi, K., Huseby, M., Schlievert, P.M., Ohlendorf, D.H., Earhart, C.A.
Deposit date:2008-08-24
Release date:2009-06-30
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (0.92 Å)
Cite:Structural Studies of an Emerging Pyrogenic Superantigen, SEK
To be Published
1P79
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CRYSTAL STRUCTURE OF A BULGED RNA TETRAPLEX: IMPLICATIONS FOR A NOVEL BINDING SITE IN RNA TETRAPLEX
Descriptor:5'-R(*UP*GP*UP*GP*GP*U)-3', POTASSIUM ION
Authors:Pan, B., Xiong, Y., Shi, K., Sundaralingam, M.
Deposit date:2003-04-30
Release date:2003-11-04
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Crystal Structure of a Bulged RNA Tetraplex at 1.1 A Resolution: Implications for a Novel Binding Site in RNA Tetraplex
STRUCTURE, 11, 2003
4EP4
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THERMUS THERMOPHILUS RUVC STRUCTURE
Descriptor:Crossover junction endodeoxyribonuclease RuvC, MAGNESIUM ION, GLYCEROL
Authors:Chen, L., Shi, K., Yin, Z.Q., Aihara, H.
Deposit date:2012-04-17
Release date:2012-11-14
Last modified:2014-12-03
Method:X-RAY DIFFRACTION (1.28 Å)
Cite:Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution.
Nucleic Acids Res., 41, 2013
1J6S
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CRYSTAL STRUCTURE OF AN RNA TETRAPLEX (UGAGGU)4 WITH A-TETRADS, G-TETRADS, U-TETRADS AND G-U OCTADS
Descriptor:5'-R(*(BRUP*GP*AP*GP*GP*U)-3', BARIUM ION, SODIUM ION
Authors:Pan, B., Xiong, Y., Shi, K., Deng, J., Sundaralingam, M.
Deposit date:2002-07-10
Release date:2003-08-05
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: implications for specific binding in RNA tetraplexes
Structure, 11, 2003
2GRB
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CRYSTAL STRUCTURE OF AN RNA QUADRUPLEX CONTAINING INOSINE-TETRAD
Descriptor:5'-R(*(U33)P*GP*IP*GP*GP*U)-3', POTASSIUM ION, STRONTIUM ION
Authors:Pan, B., Shi, K., Sundaralingam, M.
Deposit date:2006-04-24
Release date:2006-11-21
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads.
J.Mol.Biol., 363, 2006
5WFY
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CRYSTAL STRUCTURE OF DNA-BINDING DOMAIN OF THE BACTERIOPHAGE T4 LIGASE
Descriptor:DNA ligase, GLYCEROL
Authors:Shi, K., Aihara, H.
Deposit date:2017-07-13
Release date:2018-09-26
Last modified:2018-11-14
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Nucleic Acids Res., 46, 2018
1JO2
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CRYSTAL STRUCTURE OF THE B-DNA HEXAMER (CGATCG).DAUNOMYCIN COMPLEX CONTAINING A RIBOSE AT THE INTERCALATION SITE
Descriptor:5'-D(*C)-R(P*G)-D(P*AP*TP*CP*G)-3', DAUNOMYCIN
Authors:Shi, K., Pan, B., Sundaralingam, M.
Deposit date:2001-07-26
Release date:2003-07-29
Last modified:2017-10-04
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution.
Acta Crystallogr.,Sect.D, 59, 2003
1MDG
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AN ALTERNATING ANTIPARALLEL OCTAPLEX IN AN RNA CRYSTAL STRUCTURE
Descriptor:5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3', SODIUM ION, COBALT HEXAMMINE(III)
Authors:Pan, B.C., Xiong, Y., Shi, K., Sundaralingam, M.
Deposit date:2002-08-07
Release date:2003-08-12
Last modified:2011-09-28
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:An Eight-Stranded Helical Fragment in RNA Crystal Structure: Implications for Tetraplex Interaction
Structure, 11, 2003
2G91
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CRYSTAL STRUCTURE ANALYSIS OF THE AN RNA NONAMER R(GGUGCGC)D(BRC)R(C)
Descriptor:5'-R(*GP*GP*UP*GP*CP*GP*CP*(CBR)P*C-3', MAGNESIUM ION
Authors:Shi, K., Pan, B., Sundaralingam, M.
Deposit date:2006-03-04
Release date:2007-04-03
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal Structure of an RNA nonamer r(GGUGCGC)d(BrC)r(C) at 1.5 A resolution
To be Published
5CFT
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CRYSTAL STRUCTURE OF ANT(2")-IA IN COMPLEX WITH AMPCPP AND GENTAMICIN C1
Descriptor:Aminoglycoside Nucleotidyltransferase (2")-Ia, MANGANESE (II) ION, DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, ...
Authors:Rodionov, D., Bassenden, A.V., Berghuis, A.M.
Deposit date:2015-07-08
Release date:2016-03-16
Last modified:2017-11-22
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Structural Analysis of the Tobramycin and Gentamicin Clinical Resistome Reveals Limitations for Next-generation Aminoglycoside Design.
Acs Chem.Biol., 11, 2016
6CA4
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CRYSTAL STRUCTURE OF HUMANIZED D. RERIO TDP2 BY 14 MUTATIONS
Descriptor:Tyrosyl-DNA phosphodiesterase 2, MAGNESIUM ION, 1,2-ETHANEDIOL, ...
Authors:Shi, K., Aihrara, H.
Deposit date:2018-01-29
Release date:2018-05-02
Last modified:2019-02-20
Method:X-RAY DIFFRACTION (1.623 Å)
Cite:New fluorescence-based high-throughput screening assay for small molecule inhibitors of tyrosyl-DNA phosphodiesterase 2 (TDP2).
Eur J Pharm Sci, 118, 2018
6CC2
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CRYSTAL STRUCTURE OF CDC45 FROM ENTAMOEBA HISTOLYTICA
Descriptor:Cell division control protein 45 cdc45 putative, 1,2-ETHANEDIOL, CHLORIDE ION, ...
Authors:Shi, K., Kurniawan, F., Kurahashi, K., Bielinsky, A., Aihara, H.
Deposit date:2018-02-05
Release date:2018-06-27
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Crystal Structure ofEntamoeba histolyticaCdc45 Suggests a Conformational Switch that May Regulate DNA Replication.
iScience, 3, 2018
4F1H
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CRYSTAL STRUCTURE OF TDP2 FROM DANIO RERIO COMPLEXED WITH A SINGLE STRAND DNA
Descriptor:DNA (5'-D(P*TP*GP*CP*AP*G)-3'), Tyrosyl-DNA phosphodiesterase 2, PHOSPHATE ION, ...
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2012-05-06
Release date:2012-10-31
Last modified:2013-01-02
Method:X-RAY DIFFRACTION (1.662 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
5CQI
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CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
Descriptor:DNA dC-dU-editing enzyme APOBEC-3B, ZINC ION, GLYCEROL
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2015-07-21
Release date:2015-10-07
Last modified:2015-12-02
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.
J.Biol.Chem., 290, 2015
1FUF
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CRYSTAL STRUCTURE OF A 14BP RNA OLIGONUCLEOTIDE CONTAINING DOUBLE UU BULGES: A NOVEL INTRAMOLECULAR U*(AU) BASE TRIPLE
Descriptor:(5'-R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP*AP*(CBR)P*C)-3'), MAGNESIUM ION, SPERMINE
Authors:Deng, J., Xiong, Y., Sudarsanakumar, C., Shi, K., Sundaralingam, M.
Deposit date:2000-09-15
Release date:2001-11-09
Last modified:2018-01-31
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple.
RNA, 7, 2001
1R3Z
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CRYSTAL STRUCTURES OF D(GM5CGM5CGCGC) AND D(GCGCGM5CGM5C): EFFECTS OF METHYLATION ON ALTERNATING DNA OCTAMERS
Descriptor:5'-D(*GP*(5CM)P*GP*(5CM)P*GP*CP*GP*C)-3'
Authors:Shi, K., Pan, B., Tippin, D., Sundaralingam, M.
Deposit date:2003-10-03
Release date:2003-12-23
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.
Acta Crystallogr.,Sect.D, 60, 2004
5CFS
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CRYSTAL STRUCTURE OF ANT(2")-IA IN COMPLEX WITH AMPCPP AND TOBRAMYCIN
Descriptor:AAD(2''),Gentamicin 2''-nucleotidyltransferase,Gentamicin resistance protein, MANGANESE (II) ION, TOBRAMYCIN, ...
Authors:Rodionov, D., Bassenden, A.V., Berghuis, A.M.
Deposit date:2015-07-08
Release date:2016-03-16
Last modified:2017-11-22
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structural Analysis of the Tobramycin and Gentamicin Clinical Resistome Reveals Limitations for Next-generation Aminoglycoside Design.
Acs Chem.Biol., 11, 2016
5TD5
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CRYSTAL STRUCTURE OF HUMAN APOBEC3B VARIANT COMPLEXED WITH SSDNA
Descriptor:DNA dC->dU-editing enzyme APOBEC-3B, DNA (5'-D(P*TP*TP*CP*AP*T)-3'), ZINC ION, ...
Authors:Shi, K., Banerjee, S., Kurahashi, K., Aihara, H.
Deposit date:2016-09-16
Release date:2016-12-28
Last modified:2017-02-22
Method:X-RAY DIFFRACTION (1.718 Å)
Cite:Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Nat. Struct. Mol. Biol., 24, 2017
4FPV
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CRYSTAL STRUCTURE OF D. RERIO TDP2 COMPLEXED WITH SINGLE STRAND DNA PRODUCT
Descriptor:Tyrosyl-DNA phosphodiesterase 2, DNA (5'-D(P*TP*GP*CP*AP*G)-3'), SODIUM ION, ...
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2012-06-22
Release date:2012-10-31
Last modified:2017-11-15
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Nat.Struct.Mol.Biol., 19, 2012
5CQH
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CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
Descriptor:DNA dC-dU-editing enzyme APOBEC-3B, ZINC ION, 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, ...
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2015-07-21
Release date:2015-10-07
Last modified:2017-09-27
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.
J.Biol.Chem., 290, 2015
3I41
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CRYSTAL STRUCTURE OF BETA TOXIN FROM STAPHYLOCOCCUS AUREUS F277A, P278A MUTANT
Descriptor:Beta-hemolysin
Authors:Huseby, M., Shi, K., Kruse, A.C., Ohlendorf, D.H.
Deposit date:2009-07-01
Release date:2010-07-14
Last modified:2017-11-01
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Structure and biological functions of beta toxin from Staphylococcus aureus: Role of the hydrophobic beta hairpin in virulence
to be published
5SXH
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CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
Descriptor:DNA dC->dU-editing enzyme APOBEC-3B, ZINC ION, ethane-1,2-diol
Authors:Shi, K., Kurahashi, K., Aihara, H.
Deposit date:2016-08-09
Release date:2017-12-27
Last modified:2018-04-18
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.
Sci Rep, 7, 2017
5IRS
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CRYSTAL STRUCTURE OF THE PROTEASOMAL RPN13 PRU-DOMAIN
Descriptor:Proteasomal ubiquitin receptor ADRM1, 2,3-DIHYDROXY-1,4-DITHIOBUTANE
Authors:Chen, X., Shi, K., Walters, K., Aihara, H.
Deposit date:2016-03-14
Release date:2016-07-20
Last modified:2016-08-17
Method:X-RAY DIFFRACTION (1.796 Å)
Cite:Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome.
Structure, 24, 2016
1IK5
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CRYSTAL STRUCTURE OF A 14MER RNA CONTAINING DOUBLE UU BULGES IN TWO CRYSTAL FORMS: A NOVEL U*(AU) INTRAMOLECULAR BASE TRIPLE
Descriptor:5'-R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP*AP*(CBR)P*C)-3', 5'-R(*GP*GP*UP*AP*UP*UP*UP*UP*GP*GP*UP*AP*(CBR)P*C)-3', MAGNESIUM ION
Authors:Deng, J., Xiong, Y., Sudarsanakumar, C., Shi, K., Sundaralingam, M.
Deposit date:2001-05-02
Release date:2001-11-09
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple.
RNA, 7, 2001
2IP2
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STRUCTURE OF THE PYOCYANIN BIOSYNTHETIC PROTEIN PHZM
Descriptor:Probable phenazine-specific methyltransferase
Authors:Ladner, J.E., Parsons, J.F., Robinson, H., Shi, K.
Deposit date:2006-10-11
Release date:2006-10-24
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural and functional analysis of the pyocyanin biosynthetic protein PhzM from Pseudomonas aeruginosa.
Biochemistry, 46, 2007