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27 hits found for Sun

SASDFS3 – Murine transcription intermediary factor 1-beta, TRIM28 RBCC assembly-null mutation R184D

Transcription intermediary factor 1-beta experimental SAS data
GASBOR model
Sample: Transcription intermediary factor 1-beta dimer, 82 kDa Mus musculus protein
Buffer: 10 mM Tris 300 mM NaCl 0.1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Aug 10
A Dissection of Oligomerisation by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family. J Mol Biol (2019)
Sun Y, Keown JR, Black MM, Raclot C, Demarais N, Trono D, Turelli P, Goldstone DC
RgGuinier 7.0 nm
Dmax 23.2 nm
VolumePorod 232 nm3

SASDFT3 – Murine transcription intermediary factor 1-beta, TRIM28 RBCC assembly-null mutation R184D, complexed with the Krab domain of ZFP809 fused to an N-terminal MBP

Transcription intermediary factor 1-betaZinc finger protein 809 N-terminal MBP fusion experimental SAS data
GASBOR model
Sample: Transcription intermediary factor 1-beta dimer, 82 kDa Mus musculus protein
Zinc finger protein 809 N-terminal MBP fusion monomer, 52 kDa Mus musculus protein
Buffer: 10 mM Tris 300 mM NaCl 0.1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Aug 10
A Dissection of Oligomerisation by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family. J Mol Biol (2019)
Sun Y, Keown JR, Black MM, Raclot C, Demarais N, Trono D, Turelli P, Goldstone DC
RgGuinier 6.4 nm
Dmax 22.0 nm
VolumePorod 252 nm3

SASDEN4 – Protein tyrosine phosphatase SHP2

Tyrosine-protein phosphatase non-receptor type 11 experimental SAS data
ALLOSMOD model
Sample: Tyrosine-protein phosphatase non-receptor type 11 monomer, 61 kDa Homo sapiens protein
Buffer: 50 mM ADA, 2 mM TCEP, pH: 6.5
Experiment: SAXS data collected at BL4-2, Stanford Synchrotron Radiation Lightsource (SSRL) on 2016 Mar 28
Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2. Nat Commun 9(1):4507 (2018)
...Sun Y, Marko I, Pitsawong W, Stiller JB, Otten R, Kern D
RgGuinier 2.7 nm
Dmax 8.9 nm

SASDEP4 – Protein tyrosine phosphatase SHP2 with E76K activating mutation

Tyrosine-protein phosphatase non-receptor type 11 E76K experimental SAS data
ALLOSMOD model
Sample: Tyrosine-protein phosphatase non-receptor type 11 E76K monomer, 61 kDa Homo sapiens protein
Buffer: 50 mM ADA, 2 mM TCEP, pH: 6.5
Experiment: SAXS data collected at BL4-2, Stanford Synchrotron Radiation Lightsource (SSRL) on 2016 Mar 28
Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2. Nat Commun 9(1):4507 (2018)
...Sun Y, Marko I, Pitsawong W, Stiller JB, Otten R, Kern D
RgGuinier 2.9 nm
Dmax 9.5 nm

SASDQ85 – Phosphofructokinase B (PfkB) from Mycobacterium marinum

Fructokinase, PfkB experimental SAS data
DAMMIF model
Sample: Fructokinase, PfkB monomer, 32 kDa Mycobacterium marinum (strain … protein
Buffer: 20 mM Tris-HCl, 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2019 Dec 17
Structural analysis and functional study of phosphofructokinase B (PfkB) from Mycobacterium marinum Biochemical and Biophysical Research Communications (2021)
...Sun Y, Ji C, Gan J, Li J
RgGuinier 2.0 nm
Dmax 6.6 nm
VolumePorod 58 nm3

SASDAZ5 – NetrinVIV

Netrin-1 experimental SAS data
DAMMIN model
Sample: Netrin-1 monomer, 49 kDa Homo sapiens protein
Buffer: 25 MES mM 200 mM NaCl 50 mM Tris 0.2 M ammonium sulfate (NH4)2(SO4) 1mM calcium chloride CaCl2, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Aug 26
The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue. Neuron 83(4):839-849 (2014)
...Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HDT, Svergun DI, Zhang Y, Wang JH, Meijers R
RgGuinier 3.9 nm
Dmax 13.5 nm
VolumePorod 100 nm3

SASDA26 – DCC56

Deleted in Colorectal Cancer (FN5 & FN6) experimental SAS data
DAMMIN model
Sample: Deleted in Colorectal Cancer (FN5 & FN6) monomer, 26 kDa Homo sapiens protein
Buffer: 25 MES mM 200 mM NaCl 50 mM Tris 0.2 M ammonium sulfate (NH4)2(SO4) 1mM calcium chloride CaCl2, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Aug 26
The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue. Neuron 83(4):839-849 (2014)
...Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HDT, Svergun DI, Zhang Y, Wang JH, Meijers R
RgGuinier 3.2 nm
Dmax 11.0 nm
VolumePorod 38 nm3

SASDA76 – NetrinVIV DCC56 complex

Netrin-1Deleted in Colorectal Cancer (FN5 & FN6) experimental SAS data
Netrin-1 Deleted in Colorectal Cancer (FN5 & FN6) Kratky plot
Sample: Netrin-1 monomer, 49 kDa Homo sapiens protein
Deleted in Colorectal Cancer (FN5 & FN6) monomer, 26 kDa Homo sapiens protein
Buffer: 25 MES mM 200 mM NaCl 50 mM Tris 0.2 M ammonium sulfate (NH4)2(SO4) 1mM calcium chloride CaCl2, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Oct 31
The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue. Neuron 83(4):839-849 (2014)
...Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HDT, Svergun DI, Zhang Y, Wang JH, Meijers R
RgGuinier 5.1 nm
Dmax 17.0 nm
VolumePorod 120 nm3

SASDA86 – NetrinVIV DCC56(M933R) complex

Netrin-1Deleted in Colorectal Cancer (FN5 & FN6) M933R mutant experimental SAS data
Netrin-1 Deleted in Colorectal Cancer (FN5 & FN6) M933R mutant Kratky plot
Sample: Netrin-1 monomer, 49 kDa Homo sapiens protein
Deleted in Colorectal Cancer (FN5 & FN6) M933R mutant monomer, 26 kDa Homo sapiens protein
Buffer: 25 MES mM 200 mM NaCl 50 mM Tris 0.2 M ammonium sulfate (NH4)2(SO4) 1mM calcium chloride CaCl2, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Aug 26
The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue. Neuron 83(4):839-849 (2014)
...Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HDT, Svergun DI, Zhang Y, Wang JH, Meijers R
RgGuinier 4.0 nm
Dmax 14.0 nm
VolumePorod 95 nm3

SASDS67 – Complex of BCL-6 corepressor linker-PUFD bound to Polycomb group RING finger protein 1 RAWUL, Lysine-specific demethylase 2B F-box-LRRs, and S-phase kinase-associated protein 1

BCL-6 corepressorLysine-specific demethylase 2BPolycomb group RING finger protein 1S-phase kinase-associated protein 1 experimental SAS data
OTHER model
Sample: BCL-6 corepressor monomer, 16 kDa Homo sapiens protein
Lysine-specific demethylase 2B monomer, 32 kDa Homo sapiens protein
Polycomb group RING finger protein 1 monomer, 13 kDa Homo sapiens protein
S-phase kinase-associated protein 1 monomer, 19 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2022 Sep 1
Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation. Commun Biol 7(1):1112 (2024)
...Sun M, Dong Y, Yin Y, Su C, Peng C, Liu J, Xu J
RgGuinier 3.3 nm
Dmax 11.5 nm
VolumePorod 118 nm3

SASDS77 – Complex of BCL-6 corepressor ANK-linker-PUFD bound to Polycomb group RING finger protein 1 RAWUL, Lysine-specific demethylase 2B F-box-LRRs, and S-phase kinase-associated protein 1

Lysine-specific demethylase 2BPolycomb group RING finger protein 1S-phase kinase-associated protein 1BCL-6 corepressor experimental SAS data
OTHER model
Sample: Lysine-specific demethylase 2B monomer, 32 kDa Homo sapiens protein
Polycomb group RING finger protein 1 monomer, 13 kDa Homo sapiens protein
S-phase kinase-associated protein 1 monomer, 19 kDa Homo sapiens protein
BCL-6 corepressor monomer, 32 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2021 Jul 16
Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation. Commun Biol 7(1):1112 (2024)
...Sun M, Dong Y, Yin Y, Su C, Peng C, Liu J, Xu J
RgGuinier 3.9 nm
Dmax 16.5 nm
VolumePorod 190 nm3

SASDP89 – IgG Fc receptor CD64

High affinity immunoglobulin gamma Fc recombinant CD64 experimental SAS data
High affinity immunoglobulin gamma Fc recombinant CD64 Kratky plot
Sample: High affinity immunoglobulin gamma Fc recombinant CD64 monomer, 32 kDa synthetic construct protein
Buffer: 30 mM Tris, 150 mM NaCl, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Dec 9
The solution structure of the unbound IgG Fc receptor CD64 resembles its crystal structure: Implications for function. PLoS One 18(9):e0288351 (2023)
...Sun PD, Perkins SJ
RgGuinier 3.4 nm
Dmax 12.3 nm
VolumePorod 30 nm3

SASDQF9 – GRP94 protein (Endoplasmin)

Endoplasmin experimental SAS data
Endoplasmin Kratky plot
Sample: Endoplasmin dimer, 169 kDa Mus musculus protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Jul 11
Visualization of conformational transition of GRP94 in solution. Life Sci Alliance 7(2) (2024)
Sun S, Zhu R, Zhu M, Wang Q, Li N, Yang B
RgGuinier 5.6 nm
Dmax 24.0 nm
VolumePorod 260 nm3

SASDQG9 – GRP94 protein (Endoplasmin) bound to ADP

Endoplasmin experimental SAS data
Endoplasmin Kratky plot
Sample: Endoplasmin dimer, 169 kDa Mus musculus protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Jul 11
Visualization of conformational transition of GRP94 in solution. Life Sci Alliance 7(2) (2024)
Sun S, Zhu R, Zhu M, Wang Q, Li N, Yang B
RgGuinier 5.7 nm
Dmax 24.0 nm
VolumePorod 274 nm3

SASDQH9 – GRP94 protein (Endoplasmin) bound to AMP-PNP

Endoplasmin experimental SAS data
Endoplasmin Kratky plot
Sample: Endoplasmin dimer, 169 kDa Mus musculus protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Jul 11
Visualization of conformational transition of GRP94 in solution. Life Sci Alliance 7(2) (2024)
Sun S, Zhu R, Zhu M, Wang Q, Li N, Yang B
RgGuinier 5.5 nm
Dmax 24.5 nm
VolumePorod 260 nm3

SASDCT9 – Bacteriophage phi-X174 - Empty Capsid

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
Sun Y, Roznowski AP, Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 14.0 nm

SASDCU9 – Bacteriophage phi-X174 - Before Reaction with LPS

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
Sun Y, Roznowski AP, Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 12.1 nm

SASDCV9 – Bacteriophage phi-X174 - ~45s after mixing with LPS

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.15 mg/mL LPS, 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
Sun Y, Roznowski AP, Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 12.7 nm

SASDQV9 – Nanobody1 in complex with the extracellular domain of human BCMA

Tumor necrosis factor receptor superfamily member 17Nanobody1 experimental SAS data
Tumor necrosis factor receptor superfamily member 17 Nanobody1 Kratky plot
Sample: Tumor necrosis factor receptor superfamily member 17 monomer, 6 kDa Homo sapiens protein
Nanobody1 monomer, 14 kDa protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 8
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2022 Aug 28
Antigen-induced chimeric antigen receptor multimerization amplifies on-tumor cytotoxicity. Signal Transduct Target Ther 8(1):445 (2023)
Sun Y, Yang XN, Yang SS, Lyu YZ, Zhang B, Liu KW, Li N, Cui JC, Huang GX, Liu CL, Xu J, Mi JQ, Chen Z, Fan XH, Chen SJ, Chen S
RgGuinier 3.0 nm
Dmax 9.8 nm
VolumePorod 52 nm3

SASDCW9 – Bacteriophage phi-X174 - ~245s after mixing with LPS

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.15 mg/mL LPS, 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
Sun Y, Roznowski AP, Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 12.9 nm

SASDQW9 – Nanobody2 in complex with the extracellular domain of human BCMA

Tumor necrosis factor receptor superfamily member 17Nanobody2 experimental SAS data
Tumor necrosis factor receptor superfamily member 17 Nanobody2 Kratky plot
Sample: Tumor necrosis factor receptor superfamily member 17 monomer, 6 kDa Homo sapiens protein
Nanobody2 monomer, 14 kDa protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 8
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2022 Aug 28
Antigen-induced chimeric antigen receptor multimerization amplifies on-tumor cytotoxicity. Signal Transduct Target Ther 8(1):445 (2023)
Sun Y, Yang XN, Yang SS, Lyu YZ, Zhang B, Liu KW, Li N, Cui JC, Huang GX, Liu CL, Xu J, Mi JQ, Chen Z, Fan XH, Chen SJ, Chen S
RgGuinier 2.0 nm
Dmax 9.0 nm
VolumePorod 24 nm3

SASDCX9 – Bacteriophage phi-X174 - ~545s after mixing with LPS

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.15 mg/mL LPS, 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
Sun Y, Roznowski AP, Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 12.9 nm

SASDQX9 – Tandem nanobody in complex with the extracellular domain of human BCMA

Tumor necrosis factor receptor superfamily member 17Tandem nanobody experimental SAS data
Tumor necrosis factor receptor superfamily member 17 Tandem nanobody Kratky plot
Sample: Tumor necrosis factor receptor superfamily member 17 monomer, 6 kDa Homo sapiens protein
Tandem nanobody monomer, 27 kDa protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 8
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2022 Aug 28
Antigen-induced chimeric antigen receptor multimerization amplifies on-tumor cytotoxicity. Signal Transduct Target Ther 8(1):445 (2023)
Sun Y, Yang XN, Yang SS, Lyu YZ, Zhang B, Liu KW, Li N, Cui JC, Huang GX, Liu CL, Xu J, Mi JQ, Chen Z, Fan XH, Chen SJ, Chen S
RgGuinier 5.1 nm
Dmax 23.3 nm
VolumePorod 247 nm3

SASDJF5 – SUN domain of SUN1 harbouring mutation I673E - monomer

SUN domain-containing protein 1, I673E experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: SUN domain-containing protein 1, I673E monomer, 23 kDa Homo sapiens protein
Buffer: 20 mM Tris pH 8.0, 150 mM KCl, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Jul 29
...SUN-KASH 6:6 assemblies. Elife 10 (2021)
Gurusaran M, Davies OR
RgGuinier 2.1 nm
Dmax 8.2 nm
VolumePorod 42 nm3

SASDJC5 – ...SUN domain of SUN1 and KASH domain of Nesprin-4 - SUN1-KASH4 6:6 complex

SUN domain-containing protein 1Nesprin-4 experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: SUN domain-containing protein 1 hexamer, 135 kDa Homo sapiens protein
Nesprin-4 hexamer, 20 kDa Homo sapiens protein
Buffer: 20 mM Tris pH 8.0, 150 mM KCl, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 May 21
...SUN-KASH 6:6 assemblies. Elife 10 (2021)
Gurusaran M, Davies OR
RgGuinier 4.0 nm
Dmax 13.5 nm
VolumePorod 240 nm3

SASDJD5 – ...SUN domain of SUN1 and KASH domain of KASH5 - SUN1-KASH5 6:6 complex

SUN domain-containing protein 1Protein KASH5 experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: SUN domain-containing protein 1 hexamer, 135 kDa Homo sapiens protein
Protein KASH5 hexamer, 20 kDa Homo sapiens protein
Buffer: 20 mM Tris pH 8.0, 150 mM KCl, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Dec 17
...SUN-KASH 6:6 assemblies. Elife 10 (2021)
Gurusaran M, Davies OR
RgGuinier 3.8 nm
Dmax 13.5 nm
VolumePorod 244 nm3

SASDJE5 – ...SUN domain of SUN1 and KASH domain of Nesprin-1 - SUN1-KASH1 6:6 complex

SUN domain-containing protein 1Nesprin-1 experimental SAS data
CORAL model
Sample: SUN domain-containing protein 1 hexamer, 135 kDa Homo sapiens protein
Nesprin-1 hexamer, 22 kDa Homo sapiens protein
Buffer: 20 mM Tris pH 8.0, 150 mM KCl, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Dec 17
...SUN-KASH 6:6 assemblies. Elife 10 (2021)
Gurusaran M, Davies OR
RgGuinier 3.9 nm
Dmax 13.0 nm
VolumePorod 254 nm3