Solution structures of DEAD-box helicase DDX3X reveal the N-terminal extension binds RNA to modulate catalysis and influence conformation

Sarah Atkinson Submitted to SASBDB: 2023 Feb 3
Published in SASBDB:

SASDR65 – ATP-dependent RNA helicase DDX3X (amino acids 1-580)

ATP-dependent RNA helicase DDX3X (truncation; amino acids 1-580) experimental SAS data
ATP-dependent RNA helicase DDX3X (truncation; amino acids 1-580) Kratky plot
Sample: ATP-dependent RNA helicase DDX3X (truncation; amino acids 1-580) monomer, 67 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 10% (v/v) glycerol, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Jun 26
RgGuinier 3.8 nm
Dmax 13.0 nm
VolumePorod 116 nm3

SASDR75 – ATP-dependent RNA helicase DDX3X (amino acids 50-580)

ATP-dependent RNA helicase DDX3X (truncation; amino acids 50-580) experimental SAS data
ATP-dependent RNA helicase DDX3X (truncation; amino acids 50-580) Kratky plot
Sample: ATP-dependent RNA helicase DDX3X (truncation; amino acids 50-580) monomer, 62 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 10% (v/v) glycerol, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Jun 26
RgGuinier 3.6 nm
Dmax 12.9 nm
VolumePorod 102 nm3

SASDR85 – ATP-dependent RNA helicase DDX3X (amino acids 100-580)

ATP-dependent RNA helicase DDX3X (truncation; amino acids 100-580) experimental SAS data
ATP-dependent RNA helicase DDX3X (truncation; amino acids 100-580) Kratky plot
Sample: ATP-dependent RNA helicase DDX3X (truncation; amino acids 100-580) monomer, 57 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 10% (v/v) glycerol, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Jun 26
RgGuinier 3.4 nm
Dmax 10.4 nm
VolumePorod 88 nm3

SASDR95 – ATP-dependent RNA helicase DDX3X (amino acids 135-580)

ATP-dependent RNA helicase DDX3X (truncation; amino acids 135-580) experimental SAS data
DAMFILT model
Sample: ATP-dependent RNA helicase DDX3X (truncation; amino acids 135-580) monomer, 52 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 10% (v/v) glycerol, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Jun 26
RgGuinier 3.1 nm
Dmax 9.2 nm
VolumePorod 77 nm3

SASDRA5 – 15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target)

15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) experimental SAS data
DAMMIF model
Sample: 15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) dimer, 10 kDa RNA
Buffer: 20 mM Tris, 150 mM NaCl, 10% (v/v) glycerol, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Jun 26
RgGuinier 1.5 nm
Dmax 4.2 nm
VolumePorod 14 nm3

SASDRB5 – ATP-dependent RNA helicase DDX3X (amino acids 1-580) bound to a 15 nucleotide RNA duplex

ATP-dependent RNA helicase DDX3X (truncation; amino acids 1-580)15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) experimental SAS data
MONSA model
Sample: ATP-dependent RNA helicase DDX3X (truncation; amino acids 1-580) monomer, 67 kDa Homo sapiens protein
15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) dimer, 10 kDa RNA
Buffer: 20 mM Tris, 150 mM NaCl, 10% (v/v) glycerol, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Jun 26
RgGuinier 3.6 nm
Dmax 11.2 nm
VolumePorod 105 nm3

SASDRC5 – ATP-dependent RNA helicase DDX3X (amino acids 135-580) bound to a 15 nucleotide RNA duplex

ATP-dependent RNA helicase DDX3X (truncation; amino acids 135-580)15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) experimental SAS data
MONSA model
Sample: ATP-dependent RNA helicase DDX3X (truncation; amino acids 135-580) monomer, 52 kDa Homo sapiens protein
15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) dimer, 10 kDa RNA
Buffer: 20 mM Tris, 150 mM NaCl, 10% (v/v) glycerol, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Jun 26
RgGuinier 2.9 nm
Dmax 8.5 nm