MACROMOLECULE TYPE: heterocomplex

SASDUU5 – Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 bound to 3'UTR fragment of ADP-ribosylation factor 1

Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177)3'UTR fragment of ADP-ribosylation factor 1 experimental SAS data
CORAL model
Sample: Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177) dimer, 89 kDa Homo sapiens protein
3'UTR fragment of ADP-ribosylation factor 1 monomer, 14 kDa Homo sapiens RNA
Buffer: 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH: 7
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2020 May 4
A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy. Curr Protoc 5(1):e70084 (2025)
Tripepi A, Shakoor H, Klapetek P
RgGuinier 4.9 nm
Dmax 13.4 nm
VolumePorod 129 nm3

SASDUV5 – Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) motif bound to 3'UTR fragment of ADP-ribosylation factor 1

3'UTR fragment of ADP-ribosylation factor 1Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) experimental SAS data
CORAL model
Sample: 3'UTR fragment of ADP-ribosylation factor 1 monomer, 14 kDa Homo sapiens RNA
Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) dimer, 81 kDa Homo sapiens protein
Buffer: 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH: 7
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2024 Jan 12
A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy. Curr Protoc 5(1):e70084 (2025)
Tripepi A, Shakoor H, Klapetek P
RgGuinier 5.5 nm
Dmax 16.1 nm
VolumePorod 139 nm3

SASDK88 – E3 ubiquitin/ISG15 ligase TRIM25 bound to pre-let-7-a-1@1 RNA (TRIM25/pre-let-7)

E3 ubiquitin/ISG15 ligase TRIM25pre-let-7-a-1@1 experimental SAS data
E3 ubiquitin/ISG15 ligase TRIM25 pre-let-7-a-1@1 Kratky plot
Sample: E3 ubiquitin/ISG15 ligase TRIM25 dimer, 100 kDa Homo sapiens protein
Pre-let-7-a-1@1 monomer, 9 kDa synthetic construct RNA
Buffer: 20 mM MES, 75 mM NaCl, 1 mM TCEP, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 May 14
The molecular dissection of TRIM25's RNA-binding mechanism provides key insights into its antiviral activity. Nat Commun 15(1):8485 (2024)
Álvarez L, Haubrich K, Iselin L, Gillioz L, Ruscica V, Lapouge K, Augsten S, Huppertz I, Choudhury NR, Simon B, Masiewicz P, Lethier M, Cusack S, Rittinger K, Gabel F, Leitner A, Michlewski G, Hentze MW, Allain FHT, Castello A, Hennig J
RgGuinier 5.7 nm
Dmax 19.8 nm

SASDK98 – E3 ubiquitin/ISG15 ligase TRIM25 bound to pre-let-7-a-1@1 RNA (TRIM25/pre-let-7): SEC-SAXS

E3 ubiquitin/ISG15 ligase TRIM25pre-let-7-a-1@1 experimental SAS data
E3 ubiquitin/ISG15 ligase TRIM25 pre-let-7-a-1@1 Kratky plot
Sample: E3 ubiquitin/ISG15 ligase TRIM25 dimer, 100 kDa Homo sapiens protein
Pre-let-7-a-1@1 monomer, 9 kDa synthetic construct RNA
Buffer: 20 mM MES, 75 mM NaCl, 1 mM TCEP, pH: 6.5
Experiment: SAXS data collected at BM29, ESRF on 2018 Jun 4
The molecular dissection of TRIM25's RNA-binding mechanism provides key insights into its antiviral activity. Nat Commun 15(1):8485 (2024)
Álvarez L, Haubrich K, Iselin L, Gillioz L, Ruscica V, Lapouge K, Augsten S, Huppertz I, Choudhury NR, Simon B, Masiewicz P, Lethier M, Cusack S, Rittinger K, Gabel F, Leitner A, Michlewski G, Hentze MW, Allain FHT, Castello A, Hennig J
RgGuinier 5.7 nm
Dmax 23.0 nm

SASDKA8 – E3 ubiquitin/ISG15 ligase TRIM25 bound to lnczc3h7a_304-326 RNA (TRIM25/lnczc3h7a)

E3 ubiquitin/ISG15 ligase TRIM25lnczc3h7a_304-326 experimental SAS data
E3 ubiquitin/ISG15 ligase TRIM25 lnczc3h7a_304-326 Kratky plot
Sample: E3 ubiquitin/ISG15 ligase TRIM25 dimer, 100 kDa Homo sapiens protein
Lnczc3h7a_304-326 monomer, 8 kDa Homo sapiens RNA
Buffer: 20 mM MES, 75 mM NaCl, 1 mM TCEP, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 12
The molecular dissection of TRIM25's RNA-binding mechanism provides key insights into its antiviral activity. Nat Commun 15(1):8485 (2024)
Álvarez L, Haubrich K, Iselin L, Gillioz L, Ruscica V, Lapouge K, Augsten S, Huppertz I, Choudhury NR, Simon B, Masiewicz P, Lethier M, Cusack S, Rittinger K, Gabel F, Leitner A, Michlewski G, Hentze MW, Allain FHT, Castello A, Hennig J
RgGuinier 5.8 nm
Dmax 16.6 nm

SASDV54 – YdaS, a cro-type repressor from Escherichai coli O157:H7 cryptic prophage CP-933 bound to a 22 base pair dsDNA.

Phage antirepressor protein CroIR1 22 base pair dsDNA experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Phage antirepressor protein Cro dimer, 24 kDa Escherichia coli O157:H7 protein
IR1 22 base pair dsDNA monomer, 14 kDa DNA
Buffer: 20 mM sodium acetate, 150 mM NaCl, 1 mM TCEP, pH: 5.5
Experiment: SAXS data collected at BM29, ESRF on 2021 Apr 13
Structural-function relationship of YdaS, a Cro-type repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7
Marusa Prolic Kalinsek
RgGuinier 2.8 nm
Dmax 10.1 nm
VolumePorod 53 nm3

SASDU29 – The homeodomain of Cone-rod homeobox protein (CRX) bound to Ret4 of the rhodopsin promoter

Cone-rod homeobox proteinRet4 sense strandRet4 antisense strand experimental SAS data
COOT model
Sample: Cone-rod homeobox protein, 20 kDa Homo sapiens protein
Ret4 sense strand, 6 kDa synthetic construct DNA
Ret4 antisense strand, 6 kDa synthetic construct DNA
Buffer: 20 mM Tris, 150 mM KCl, 5 % glycerol, 1 mM TCEP, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Mar 25
Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element Structure (2024)
Srivastava D, Gowribidanur-Chinnaswamy P, Gaur P, Spies M, Swaroop A, Artemyev N
RgGuinier 2.2 nm
Dmax 6.8 nm
VolumePorod 37 nm3

SASDS86 – Antitoxin HigA-2 in complex with a DNA operator sequence

Antitoxin HigA-2DNA operator experimental SAS data
Antitoxin HigA-2 DNA operator Kratky plot
Sample: Antitoxin HigA-2 dimer, 23 kDa Vibrio cholerae serotype … protein
DNA operator dimer, 20 kDa DNA
Buffer: 20 mM Tris pH 8, 200 mM NaCl, pH: 8
Experiment: SAXS data collected at SWING, SOLEIL on 2013 Apr 6
Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 15(1):3105 (2024)
Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haeserts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R
RgGuinier 2.7 nm
Dmax 9.6 nm
VolumePorod 57 nm3

SASDRX8 – Heterodimeric complex of AfAgo protein Af1318 and AfAgo-N protein (containing N-L1-L2 domains) with a 14 base pair DNA oligoduplex in low salt buffer

Piwi protein AF_1318 (Archaeoglobus fulgidus AfAgo protein)Uncharacterized protein (AfAgo-N protein containing N-L1-L2 domains)5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Piwi protein AF_1318 (Archaeoglobus fulgidus AfAgo protein) monomer, 51 kDa Archaeoglobus fulgidus (strain … protein
Uncharacterized protein (AfAgo-N protein containing N-L1-L2 domains) monomer, 31 kDa Archaeoglobus fulgidus DSM … protein
5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) monomer, 9 kDa DNA
Buffer: 20 mM TrisHCl pH 7.5, 200 mM NaCl, 5 mM MgCl2, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 6
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res (2024)
Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M
RgGuinier 2.9 nm
Dmax 9.7 nm
VolumePorod 145 nm3

SASDRY8 – Single-chain Archaeoglobus fulgidus argonaute fAfAgo-fusion variant complexed with a 14 base pair DNA oligoduplex in low salt buffer

single-chain full Archaeoglobus fulgidus Argonaute5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) experimental SAS data
GASBOR model
Sample: Single-chain full Archaeoglobus fulgidus Argonaute monomer, 78 kDa Archaeoglobus fulgidus protein
5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) monomer, 9 kDa DNA
Buffer: 20 mM TrisHCl pH7.5, 200 mM NaCl, 5 mM MgCl2, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 6
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res (2024)
Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M
RgGuinier 3.0 nm
Dmax 10.3 nm
VolumePorod 131 nm3