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15 hits found for Liang

SASDPD3 – Second exon splicing silencer 2p (ESS2p) RNA, apo

The second exon splicing silencer 2p experimental SAS data
AMBER model
Sample: The second exon splicing silencer 2p monomer, 14 kDa RNA
Buffer: 20 mM Bis-Tris, 20 mM NaCl, pH: 6.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Nov 1
Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors. J Mol Biol 434(18):167728 (2022)
Chiu LY, Emery A, Jain N, Sugarman A, Kendrick N, Luo L, Ford W, Swanstrom R, Tolbert BS
RgGuinier 2.1 nm
Dmax 6.9 nm
VolumePorod 21 nm3

SASDKK3 – SEC-SAXS of Presequence Protease (PreP)

Presequence protease, mitochondrial experimental SAS data
Presequence protease, mitochondrial Kratky plot
Sample: Presequence protease, mitochondrial monomer, 115 kDa Homo sapiens protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 7.7
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Mar 4
Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition Nature Communications 13(1) (2022)
Liang W, Wijaya J, Wei H, Noble A, Mancl J, Mo S, Lee D, Lin King J, Pan M, Liu C, Koehler C, Zhao M, Potter C, Carragher B, Li S, Tang W
RgGuinier 3.2 nm
Dmax 9.1 nm
VolumePorod 170 nm3

SASDBL3 – Highly similar to Actin cross-linking family protein 7 (ACF7) Homo Sapiens

cDNA FLJ45612 fis, clone BRTHA3025073, highly similar to Actin cross-linking family protein 7 experimental SAS data
cDNA FLJ45612 fis, clone BRTHA3025073, highly similar to Actin cross-linking family protein 7 Kratky plot
Sample: cDNA FLJ45612 fis, clone BRTHA3025073, highly similar to Actin cross-linking family protein 7 monomer, 46 kDa Homo sapiens protein
Buffer: PBS, pH: 7.4
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2014 Nov 10
In vivo epidermal migration requires focal adhesion targeting of ACF7. Nat Commun 7:11692 (2016)
...Liang WG, Gou X, Lee P, Liu H, Lyu W, Tang WJ, Chen SY, Yang F, Liang H, Wu X
RgGuinier 3.4 nm
Dmax 13.5 nm
VolumePorod 53 nm3

SASDKL3 – SEC-SAXS of Presequence Protease (PreP) with inhibitor MitoBloCK-60 (MB-60)

Presequence protease, mitochondrial experimental SAS data
Presequence protease, mitochondrial Kratky plot
Sample: Presequence protease, mitochondrial monomer, 115 kDa Homo sapiens protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 7.7
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Mar 7
Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition Nature Communications 13(1) (2022)
Liang W, Wijaya J, Wei H, Noble A, Mancl J, Mo S, Lee D, Lin King J, Pan M, Liu C, Koehler C, Zhao M, Potter C, Carragher B, Li S, Tang W
RgGuinier 3.1 nm
Dmax 9.1 nm
VolumePorod 165 nm3

SASDKM3 – SEC-SAXS of Presequence Protease (PreP) with pre-sequence of citrate synthase (1-27)

Presequence protease, mitochondrialCitrate synthase, mitochondrial experimental SAS data
Presequence protease, mitochondrial Citrate synthase, mitochondrial Kratky plot
Sample: Presequence protease, mitochondrial monomer, 115 kDa Homo sapiens protein
Citrate synthase, mitochondrial monomer, 3 kDa Homo sapiens protein
Buffer: 20 mM Tris, 100 mM NaCl , 20 mM EDTA, pH: 7.7
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Nov 4
Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition Nature Communications 13(1) (2022)
Liang W, Wijaya J, Wei H, Noble A, Mancl J, Mo S, Lee D, Lin King J, Pan M, Liu C, Koehler C, Zhao M, Potter C, Carragher B, Li S, Tang W
RgGuinier 3.1 nm
Dmax 8.7 nm
VolumePorod 165 nm3

SASDBN3 – Highly similar to Actin cross-linking family protein 7 (ACF7) Y259D mutant Homo Sapiens

cDNA FLJ45612 fis, clone BRTHA3025073, highly similar to Actin cross-linking family protein 7 Y259D mutant experimental SAS data
cDNA FLJ45612 fis, clone BRTHA3025073, highly similar to Actin cross-linking family protein 7 Y259D mutant Kratky plot
Sample: cDNA FLJ45612 fis, clone BRTHA3025073, highly similar to Actin cross-linking family protein 7 Y259D mutant monomer, 46 kDa Homo sapiens protein
Buffer: PBS, pH: 7.4
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2014 Nov 7
In vivo epidermal migration requires focal adhesion targeting of ACF7. Nat Commun 7:11692 (2016)
...Liang WG, Gou X, Lee P, Liu H, Lyu W, Tang WJ, Chen SY, Yang F, Liang H, Wu X
RgGuinier 3.4 nm
Dmax 13.5 nm
VolumePorod 55 nm3

SASDKN3 – SEC-SAXS of Presequence Protease (PreP) with Amyloid beta precursor protein (1-40)

Presequence protease, mitochondrialAmyloid-beta precursor protein experimental SAS data
Presequence protease, mitochondrial Amyloid-beta precursor protein Kratky plot
Sample: Presequence protease, mitochondrial monomer, 115 kDa Homo sapiens protein
Amyloid-beta precursor protein monomer, 4 kDa Homo sapiens protein
Buffer: 20 mM Tris, 100 mM NaCl , 20 mM EDTA, pH: 7.7
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Mar 7
Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition Nature Communications 13(1) (2022)
Liang W, Wijaya J, Wei H, Noble A, Mancl J, Mo S, Lee D, Lin King J, Pan M, Liu C, Koehler C, Zhao M, Potter C, Carragher B, Li S, Tang W
RgGuinier 3.0 nm
Dmax 8.5 nm
VolumePorod 175 nm3

SASDMR6 – 5-10-5 gapmer phosphorothioate antisense oligonucleotide

5-10-5 gapmer phosphorothioate antisense oligonucleotide experimental SAS data
DAMFILT model
Sample: 5-10-5 gapmer phosphorothioate antisense oligonucleotide dimer, 14 kDa
Buffer: 20 mM Tris-Cl (pH 7.5), 250 mM KCl, 50 mM L-proline, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Apr 28
Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1. Nucleic Acids Res (2021)
...Liang XH, Deplazes E, Conte MR, Marshall AC, Lee M, Fox AH, Bond CS
RgGuinier 1.8 nm
Dmax 8.5 nm
VolumePorod 15 nm3

SASDMS6 – Non-POU domain-containing octamer-binding protein (NONO homodimer)

Non-POU domain-containing octamer-binding protein experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Non-POU domain-containing octamer-binding protein dimer, 60 kDa Homo sapiens protein
Buffer: 20 mM Tris-Cl (pH 7.5), 250 mM KCl, 50 mM L-proline, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Apr 28
Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1. Nucleic Acids Res (2021)
...Liang XH, Deplazes E, Conte MR, Marshall AC, Lee M, Fox AH, Bond CS
RgGuinier 2.8 nm
Dmax 9.5 nm
VolumePorod 96 nm3

SASDMT6 – Non-POU domain-containing octamer-binding protein (NONO homodimer) bound to an antisense oligonucleotide

Non-POU domain-containing octamer-binding protein5-10-5 gapmer phosphorothioate antisense oligonucleotide tetramer experimental SAS data
SASREF model
Sample: Non-POU domain-containing octamer-binding protein dimer, 60 kDa Homo sapiens protein
5-10-5 gapmer phosphorothioate antisense oligonucleotide tetramer tetramer, 28 kDa
Buffer: 20 mM Tris-Cl (pH 7.5), 250 mM KCl, 50 mM L-proline, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Apr 28
Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1. Nucleic Acids Res (2021)
...Liang XH, Deplazes E, Conte MR, Marshall AC, Lee M, Fox AH, Bond CS
RgGuinier 3.9 nm
Dmax 18.4 nm
VolumePorod 153 nm3

SASDMM9 – Response Regulator RocR from Pseudomonas aeruginosa

RocR experimental SAS data
OTHER model
Sample: RocR tetramer, 171 kDa Pseudomonas aeruginosa (strain … protein
Buffer: 50 mM Tris–HCl, 250 mM NaCl, 10 mM imidazole, 5% glycerol, 0.5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Dec 9
Structural Insights into the Regulatory Mechanism of the Response Regulator RocR from Pseudomonas aeruginosa in Cyclic Di-GMP Signaling Journal of Bacteriology 194(18):4837-4846 (2012)
...Liang Z, Lescar J
RgGuinier 3.7 nm
Dmax 11.0 nm

SASDQ59 – Mutant 7-deazapurine in DNA protein A (D95A)

DNA-guanine transglycosylase - D95A mutant experimental SAS data
GROMACS model
Sample: DNA-guanine transglycosylase - D95A mutant monomer, 50 kDa Salmonella enterica subsp. … protein
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
...Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 2.7 nm
Dmax 10.1 nm
VolumePorod 67 nm3

SASDQ89 – 7-deazapurine in DNA protein B

DGQHR domain-containing protein experimental SAS data
ALPHAFOLD model
Sample: DGQHR domain-containing protein dimer, 88 kDa Salmonella enterica subsp. … protein
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
...Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 3.4 nm
Dmax 13.5 nm
VolumePorod 126 nm3

SASDQ79 – Mutant 7-deazapurine in DNA protein A (D95A) bound to a 28 base pair DNA substrate (2-state model: complex plus free DNA)

Custom 28 base pair double stranded DNADNA-guanine transglycosylase - D95A mutant experimental SAS data
GROMACS model
Sample: Custom 28 base pair double stranded DNA monomer, 17 kDa Synthetic, purchased from … DNA
DNA-guanine transglycosylase - D95A mutant monomer, 50 kDa Salmonella enterica subsp. … protein
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
...Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 3.4 nm
Dmax 13.5 nm
VolumePorod 104 nm3

SASDQ69 – 28 base pair DNA substrate (used in experiments with 7-deazapurine in DNA proteins)

Custom 28 base pair double stranded DNA experimental SAS data
GROMACS model
Sample: Custom 28 base pair double stranded DNA monomer, 17 kDa Synthetic, purchased from … DNA
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
...Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 2.6 nm
Dmax 10.2 nm
VolumePorod 24 nm3