Browse by MODEL: Hybrid

SASDXB4 – Peroxisomal biogenesis factor 8 (Pex8) bound to the N-terminal domain of Peroxisomal targeting signal receptor, Pex5 (Pex8-Pex5NTD complex from P. pastoris)

Peroxisomal biogenesis factor 8Peroxisomal targeting signal receptor experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Peroxisomal biogenesis factor 8 monomer, 78 kDa Komagataella pastoris protein
Peroxisomal targeting signal receptor monomer, 32 kDa Komagataella pastoris protein
Buffer: 50 mM HEPES, 150 mM NaCl, 3% v/v glycerol, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Aug 17
Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation (2025)
Ekal L, Wendscheck D, David Y, Chojnowski G, Jeffries C, Mullapudi E, Schuldiner M, Warscheid B, Zalckvar E, Wilmanns M
RgGuinier 4.6 nm
Dmax 19.0 nm
VolumePorod 177 nm3

SASDXC4 – Peroxisomal biogenesis factor 8 (Pex8) bound to the C-terminal domain of Peroxisomal targeting signal receptor, Pex5 (Pex8-Pex5CTD complex from P. pastoris)

Peroxisomal biogenesis factor 8Peroxisomal targeting signal receptor experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Peroxisomal biogenesis factor 8 monomer, 78 kDa Komagataella pastoris protein
Peroxisomal targeting signal receptor monomer, 36 kDa Komagataella pastoris protein
Buffer: 50 mM HEPES, 150 mM NaCl, 3% v/v glycerol, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Aug 17
Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation (2025)
Ekal L, Wendscheck D, David Y, Chojnowski G, Jeffries C, Mullapudi E, Schuldiner M, Warscheid B, Zalckvar E, Wilmanns M
RgGuinier 4.2 nm
Dmax 14.5 nm
VolumePorod 141 nm3

SASDXZ7 – SmThrRS model for open state based on PDB entry 6vu9

Stenotrophomonas maltophilia threonyl tRNA synthetase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Stenotrophomonas maltophilia threonyl tRNA synthetase dimer, 146 kDa Stenotrophomonas maltophilia (strain … protein
Buffer: 20 mM HEPES, 0.2 M NaCl, 1.5% v/v glycerol, and 1 mM TCEP, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2024 Nov 7
Crystal structure of a complete threonyl tRNA synthetase: toggle clamp model? Biochemical and Biophysical Research Communications :152677 (2025)
Tran T, Fenwick M, Edwards T, Dranow D, Abendroth J, Shek R, Tillery L, Craig J, Van Voorhis W, Myler P
RgGuinier 4.2 nm
Dmax 16.2 nm

SASDX28 – SmThrRS model for closed state based on PDB entry 1qf6

Stenotrophomonas maltophilia threonyl tRNA synthetase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Stenotrophomonas maltophilia threonyl tRNA synthetase dimer, 146 kDa Stenotrophomonas maltophilia (strain … protein
Buffer: 20 mM HEPES, 0.2 M NaCl, 1.5% v/v glycerol, and 1 mM TCEP, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2024 Nov 7
Crystal structure of a complete threonyl tRNA synthetase: toggle clamp model? Biochemical and Biophysical Research Communications :152677 (2025)
Tran T, Fenwick M, Edwards T, Dranow D, Abendroth J, Shek R, Tillery L, Craig J, Van Voorhis W, Myler P
RgGuinier 4.2 nm
Dmax 16.2 nm

SASDX38 – SmThrRS model for closed state based on PDB entry 1nyr

Stenotrophomonas maltophilia threonyl tRNA synthetase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Stenotrophomonas maltophilia threonyl tRNA synthetase dimer, 146 kDa Stenotrophomonas maltophilia (strain … protein
Buffer: 20 mM HEPES, 0.2 M NaCl, 1.5% v/v glycerol, and 1 mM TCEP, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2024 Nov 7
Crystal structure of a complete threonyl tRNA synthetase: toggle clamp model? Biochemical and Biophysical Research Communications :152677 (2025)
Tran T, Fenwick M, Edwards T, Dranow D, Abendroth J, Shek R, Tillery L, Craig J, Van Voorhis W, Myler P
RgGuinier 4.2 nm
Dmax 16.2 nm

SASDX48 – SmThrRS model based on PDB entries 6vu9 and 1qf6

Stenotrophomonas maltophilia threonyl tRNA synthetase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Stenotrophomonas maltophilia threonyl tRNA synthetase dimer, 146 kDa protein
Buffer: 20 mM HEPES, 0.2 M NaCl, 1.5% v/v glycerol, and 1 mM TCEP, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2024 Nov 7
Crystal structure of a complete threonyl tRNA synthetase: toggle clamp model? Biochemical and Biophysical Research Communications :152677 (2025)
Tran T, Fenwick M, Edwards T, Dranow D, Abendroth J, Shek R, Tillery L, Craig J, Van Voorhis W, Myler P
RgGuinier 4.2 nm

SASDVV4 – ST9a RNA, WT (54 nucleotides in 10 mM MgCl2; monomer)

ST9 WT (54 nt RNA) experimental SAS data
PYMOL model
Sample: ST9 WT (54 nt RNA) monomer, 17 kDa RNA
Buffer: 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 10 mM MgCl2, 0.0002% w/v NaN3, pH:
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2024 Mar 23
A conserved viral RNA fold enables nuclease resistance across kingdoms of life. Nucleic Acids Res 53(16) (2025)
Gezelle JG, Korn SM, McDonald JT, Gong Z, Erickson A, Huang CH, Yang F, Cronin M, Kuo YW, Wimberly BT, Steckelberg AL
RgGuinier 1.9 nm
Dmax 5.8 nm
VolumePorod 21 nm3

SASDVW4 – ST9a RNA, WT (54 nucleotides in 1 mM MgCl2; monomer)

ST9 WT (54 nt RNA) experimental SAS data
PYMOL model
Sample: ST9 WT (54 nt RNA) monomer, 17 kDa RNA
Buffer: 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 1 mM MgCl2, pH:
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2024 Mar 23
A conserved viral RNA fold enables nuclease resistance across kingdoms of life. Nucleic Acids Res 53(16) (2025)
Gezelle JG, Korn SM, McDonald JT, Gong Z, Erickson A, Huang CH, Yang F, Cronin M, Kuo YW, Wimberly BT, Steckelberg AL
RgGuinier 1.7 nm
Dmax 5.8 nm
VolumePorod 20 nm3

SASDVX4 – ST9a RNA, WT (59 nucleotides in 10 mM MgCl2; monomer)

ST9 WT (59 nt RNA) experimental SAS data
PYMOL model
Sample: ST9 WT (59 nt RNA) monomer, 19 kDa RNA
Buffer: 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 10 mM MgCl2, 0.0002% w/v NaN3, pH:
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2024 Jan 30
A conserved viral RNA fold enables nuclease resistance across kingdoms of life. Nucleic Acids Res 53(16) (2025)
Gezelle JG, Korn SM, McDonald JT, Gong Z, Erickson A, Huang CH, Yang F, Cronin M, Kuo YW, Wimberly BT, Steckelberg AL
RgGuinier 1.9 nm
Dmax 6.7 nm
VolumePorod 24 nm3

SASDVY4 – ST9a RNA, WT (59 nucleotides in 0 mM MgCl2; monomer)

ST9 WT (59 nt RNA) experimental SAS data
PYMOL model
Sample: ST9 WT (59 nt RNA) monomer, 19 kDa RNA
Buffer: 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 0.0002% w/v NaN3, pH:
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2024 Jan 30
A conserved viral RNA fold enables nuclease resistance across kingdoms of life. Nucleic Acids Res 53(16) (2025)
Gezelle JG, Korn SM, McDonald JT, Gong Z, Erickson A, Huang CH, Yang F, Cronin M, Kuo YW, Wimberly BT, Steckelberg AL
RgGuinier 2.1 nm
Dmax 8.3 nm
VolumePorod 26 nm3