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22 hits found for Xiao

SASDK92 – Interferon-activable protein 204 from Mus musculus (Mouse) amino-acids 215-619

Interferon-activable protein 204 experimental SAS data
CHIMERA model
Sample: Interferon-activable protein 204 monomer, 47 kDa Mus musculus protein
Buffer: 20 mM HEPES, 100 mM KCl, pH: 7.4
Experiment: SAXS data collected at X9A, National Synchrotron Light Source (NSLS) on 2013 Mar 14
Structural mechanism of DNA recognition by the p204 HIN domain. Nucleic Acids Res (2021)
...Xiao TS, Jin T
RgGuinier 3.1 nm
Dmax 9.5 nm
VolumePorod 28 nm3

SASDEE2 – The N-terminal domain of estrogen receptor alpha

Estrogen receptor experimental SAS data
CUSTOM IN-HOUSE model
Sample: Estrogen receptor monomer, 20 kDa Homo sapiens protein
Buffer: 20 mM sodium phosphate, 50 mM NaCl, 0.05 mM TCEP, pH: 7.4
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2017 Jun 12
A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain. Structure 27(2):229-240.e4 (2019)
...Xiao X, Du Z, Hsieh A, Ko S, Chen Y, Agrawal P, Zheng W, Shi W, Jiang W, Yang L, Chance MR, Surewicz WK, Buck M, Yang S
RgGuinier 3.0 nm
Dmax 10.0 nm

SASDBR3 – Wild type RNF8 complexed with Ubc13 (C87K, K92A mutant): conjugated to Ubiquitin

E3 ubiquitin-protein ligase RNF8Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)Polyubiquitin-C experimental SAS data
MES-FOXS model
Sample: E3 ubiquitin-protein ligase RNF8 dimer, 35 kDa Homo sapiens protein
Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) dimer, 36 kDa Homo sapiens protein
Polyubiquitin-C dimer, 17 kDa Homo sapiens protein
Buffer: 20 mM HEPES 200 mM NaCl 0.01 mM ZnSO4 1 mM DTT, pH: 6.8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Sep 8
RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment. J Biol Chem 291(18):9396-410 (2016)
...Xiao AT, Tainer JA, Hendzel MJ, Glover JN
RgGuinier 4.5 nm
Dmax 18.9 nm
VolumePorod 119 nm3

SASDBS3 – Wild type RNF8 complexed with Ubc13 (C87K, K92A mutant) and Mms2: conjugated to Ubiquitin

E3 ubiquitin-protein ligase RNF8Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)Polyubiquitin-CUbiquitin-conjugating enzyme E2 variant 2 experimental SAS data
MES-FOXS model
Sample: E3 ubiquitin-protein ligase RNF8 dimer, 35 kDa Homo sapiens protein
Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) dimer, 36 kDa Homo sapiens protein
Polyubiquitin-C dimer, 17 kDa Homo sapiens protein
Ubiquitin-conjugating enzyme E2 variant 2 dimer, 34 kDa Homo sapiens protein
Buffer: 20 mM HEPES 200 mM NaCl 0.01 mM ZnSO4 1 mM DTT, pH: 6.8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Sep 8
RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment. J Biol Chem 291(18):9396-410 (2016)
...Xiao AT, Tainer JA, Hendzel MJ, Glover JN
RgGuinier 5.4 nm
Dmax 23.8 nm
VolumePorod 214 nm3

SASDBT3 – RNF8 (L451D mutant) complexed with Ubc13 (C87K, K92A mutant): conjugated to Ubiquitin

Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)Polyubiquitin-CE3 ubiquitin-protein ligase RNF8 mutant (L451D) experimental SAS data
MES-FOXS model
Sample: Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) dimer, 36 kDa Homo sapiens protein
Polyubiquitin-C dimer, 17 kDa Homo sapiens protein
E3 ubiquitin-protein ligase RNF8 mutant (L451D) dimer, 35 kDa Homo sapiens protein
Buffer: 20 mM HEPES 200 mM NaCl 0.01 mM ZnSO4 1 mM DTT, pH: 6.8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Sep 8
RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment. J Biol Chem 291(18):9396-410 (2016)
...Xiao AT, Tainer JA, Hendzel MJ, Glover JN
RgGuinier 4.3 nm
Dmax 18.9 nm
VolumePorod 111 nm3

SASDBU3 – RNF8 (L451D mutant) complexed with Ubc13 (C87K, K92A mutant) and Mms2: conjugated to Ubiquitin

Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)Polyubiquitin-CUbiquitin-conjugating enzyme E2 variant 2E3 ubiquitin-protein ligase RNF8 mutant (L451D) experimental SAS data
MES-FOXS model
Sample: Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) dimer, 36 kDa Homo sapiens protein
Polyubiquitin-C dimer, 17 kDa Homo sapiens protein
Ubiquitin-conjugating enzyme E2 variant 2 dimer, 34 kDa Homo sapiens protein
E3 ubiquitin-protein ligase RNF8 mutant (L451D) dimer, 35 kDa Homo sapiens protein
Buffer: 20 mM HEPES 200 mM NaCl 0.01 mM ZnSO4 1 mM DTT, pH: 6.8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Sep 8
RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment. J Biol Chem 291(18):9396-410 (2016)
...Xiao AT, Tainer JA, Hendzel MJ, Glover JN
RgGuinier 5.2 nm
Dmax 23.8 nm
VolumePorod 192 nm3

SASDKX6 – PSK, an antimicrobial peptide from Chrysomya megacephala

PSK, an antimicrobial peptide from Chrysomya megacephala experimental SAS data
DAMMIF model
Sample: PSK, an antimicrobial peptide from Chrysomya megacephala monomer, 10 kDa Chrysomya megacephala protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Dec 7
Crystal and solution structures of a novel antimicrobial peptide from Chrysomya megacephala. Acta Crystallogr D Struct Biol 77(Pt 7):894-903 (2021)
Xiao C, Xiao Z, Hu C, Lu J, Cui L, Zhang Y, Dai Y, Zhang Q, Wang S, Liu W
RgGuinier 1.6 nm
Dmax 5.0 nm
VolumePorod 18 nm3

SASDBZ6 – Draxin

Draxin experimental SAS data
Draxin Rg histogram
Sample: Draxin monomer, 45 kDa Homo sapiens protein
Buffer: 20 mM HEPES 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Aug 19
Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC. Neuron 97(6):1261-1267.e4 (2018)
...Xiao J, Zhang Y, Wang JH, Meijers R
RgGuinier 4.2 nm
Dmax 15.0 nm
VolumePorod 87 nm3

SASDMJ9 – Plasmid pET11d- 229E710 encoding C-terminally His6-tagged HCoV-229E Nsp7-10 polyprotein

Replicase polyprotein 1a experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Replicase polyprotein 1a dimer, 19 kDa Severe acute respiratory … protein
Buffer: 10 mM Tris-HCl, 200 mM NaCl, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Apr 2
Nonstructural Proteins 7 and 8 of Feline Coronavirus Form a 2:1 Heterotrimer That Exhibits Primer-Independent RNA Polymerase Activity Journal of Virology 86(8):4444-4454 (2012)
Xiao Y, Ma Q, Restle T, Shang W, Svergun D, Ponnusamy R, Sczakiel G, Hilgenfeld R
RgGuinier 2.1 nm

SASDMK9 – Nonstructural Proteins 7 and 8 of Feline Coronavirus (complex 1:2)

Replicase polyprotein 1aReplicase polyprotein 1a experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Replicase polyprotein 1a dimer, 19 kDa Severe acute respiratory … protein
Replicase polyprotein 1a monomer, 22 kDa Severe acute respiratory … protein
Buffer: 10 mM Tris-HCl, 200 mM NaCl, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Apr 2
Nonstructural Proteins 7 and 8 of Feline Coronavirus Form a 2:1 Heterotrimer That Exhibits Primer-Independent RNA Polymerase Activity Journal of Virology 86(8):4444-4454 (2012)
Xiao Y, Ma Q, Restle T, Shang W, Svergun D, Ponnusamy R, Sczakiel G, Hilgenfeld R
RgGuinier 3.0 nm

SASDH38 – Wildtype preQ1 riboswitch in Bacillus subtilis, apo-state - Bsu-WT-apo

wildtype preQ1 riboswitch in Bacillus subtilis experimental SAS data
wildtype preQ1 riboswitch in Bacillus subtilis Kratky plot
Sample: wildtype preQ1 riboswitch in Bacillus subtilis monomer, 11 kDa Bacillus subtilis RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 2.6 nm
Dmax 10.5 nm
VolumePorod 20 nm3

SASDH48 – Wildtype preQ1 riboswitch in Bacillus subtilis, holo-state - Bsu-WT-holo

wildtype preQ1 riboswitch in Bacillus subtilis experimental SAS data
wildtype preQ1 riboswitch in Bacillus subtilis Kratky plot
Sample: wildtype preQ1 riboswitch in Bacillus subtilis monomer, 11 kDa Bacillus subtilis RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 2.0 nm
Dmax 9.0 nm
VolumePorod 16 nm3

SASDH58 – C15 deletion preQ1 riboswitch in Bacillus subtilis, apo-state - Bsu-C15d-apo

C15 deletion preQ1 riboswitch in Bacillus subtilis experimental SAS data
C15 deletion preQ1 riboswitch in Bacillus subtilis Kratky plot
Sample: C15 deletion preQ1 riboswitch in Bacillus subtilis monomer, 11 kDa Bacillus subtilis RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 1.9 nm
Dmax 8.0 nm
VolumePorod 17 nm3

SASDH68 – C15 deletion preQ1 riboswitch in Bacillus subtilis, holo-state - Bsu-C15d-holo

C15 deletion preQ1 riboswitch in Bacillus subtilis experimental SAS data
C15 deletion preQ1 riboswitch in Bacillus subtilis Kratky plot
Sample: C15 deletion preQ1 riboswitch in Bacillus subtilis monomer, 11 kDa Bacillus subtilis RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 2.0 nm
Dmax 8.8 nm
VolumePorod 14 nm3

SASDH78 – Wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis, apo-state - Tte-WT-apo

wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis experimental SAS data
wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis Kratky plot
Sample: wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis monomer, 11 kDa Caldanaerobacter subterraneus subsp. … RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 1.6 nm
Dmax 6.7 nm
VolumePorod 12 nm3

SASDH88 – Wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis, holo-state - Tte-WT-holo

wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis experimental SAS data
wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis Kratky plot
Sample: wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis monomer, 11 kDa Caldanaerobacter subterraneus subsp. … RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 1.6 nm
Dmax 7.2 nm
VolumePorod 13 nm3

SASDHB8 – A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis, apo-state - Tte-A14'-apo

A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis experimental SAS data
A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis Kratky plot
Sample: A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis monomer, 11 kDa Caldanaerobacter subterraneus subsp. … RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 1.9 nm
Dmax 9.0 nm
VolumePorod 14 nm3

SASDHC8 – A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis, holo-state - Tte-A14'-holo

A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis experimental SAS data
A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis Kratky plot
Sample: A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis monomer, 11 kDa Caldanaerobacter subterraneus subsp. … RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 1.8 nm
Dmax 12.0 nm
VolumePorod 16 nm3

SASDH98 – Wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis, apo-state high-temperature sampling - Tte-WT-apo-HT

wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis experimental SAS data
wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis Kratky plot
Sample: wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis monomer, 11 kDa Caldanaerobacter subterraneus subsp. … RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 1.7 nm
Dmax 7.0 nm
VolumePorod 11 nm3

SASDHA8 – Wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis, holo-state high-temperature sampling - Tte-WT-holo-HT

wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis experimental SAS data
wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis Kratky plot
Sample: wildtype preQ1 riboswitch in Thermoanaerobacter tengcongensis monomer, 11 kDa Caldanaerobacter subterraneus subsp. … RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 1.5 nm
Dmax 6.5 nm
VolumePorod 10 nm3

SASDHD8 – A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis, apo-state high-temperature sampling - Tte-A14'-apo-HT

A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis experimental SAS data
A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis Kratky plot
Sample: A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis monomer, 11 kDa Caldanaerobacter subterraneus subsp. … RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 1.8 nm
Dmax 7.5 nm
VolumePorod 13 nm3

SASDHE8 – A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis, holo-state high-temperature sampling - Tte-A14'-holo-HT

A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis experimental SAS data
A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis Kratky plot
Sample: A14 insertion preQ1 riboswitch in Thermoanaerobacter tengcongensis monomer, 11 kDa Caldanaerobacter subterraneus subsp. … RNA
Buffer: 50 mM potassium phosphate, 2 mM MgCl2, 50 mM KCl, pH: 6.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches. J Mol Biol 432(16):4523-4543 (2020)
...Xiao Y, Tang C
RgGuinier 1.9 nm
Dmax 8.8 nm
VolumePorod 14 nm3