Small Angle Scattering Biological Data Bank SASBDB

MACROMOLECULE TYPE: heterocomplex

SASDRZ8 – Single-chain Archaeoglobus fulgidus argonaute fAfAgo-fusion variant complexed with an 11 base pair DNA oligoduplex in low salt buffer

single-chain full Archaeoglobus fulgidus Argonaute5'-end phosphorylated DNA guide strand, 11 nt (MZ864)DNA target strand, 11 nt (MZ865) experimental SAS data

Sample:	Single-chain full Archaeoglobus fulgidus Argonaute monomer, 78 kDa Archaeoglobus fulgidus protein 5'-end phosphorylated DNA guide strand, 11 nt (MZ864) monomer, 3 kDa DNA DNA target strand, 11 nt (MZ865) monomer, 3 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 2017 Aug 31

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

R_g^Guinier	2.9	nm
D_max	9.6	nm
Volume^Porod	125	nm³

SASDPK3 – Vibrio cholerae ParD2:ParE2 complex bound to 21-bp DNA operator box

Antitoxin ParDToxin21-bp DNA operator fragment experimental SAS data

Sample:	Antitoxin ParD hexamer, 54 kDa Vibrio cholerae serotype … protein Toxin, 25 kDa Vibrio cholerae serotype … protein 21-bp DNA operator fragment monomer, 13 kDa Vibrio cholerae O1 DNA
Buffer:	20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH: 8
Experiment:	SAXS data collected at SWING, SOLEIL on 2020 Jul 18

Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module. Sci Adv 10(1):eadj2403 (2024)
Garcia-Rodriguez G, Girardin Y, Kumar Singh R, Volkov AN, Van Dyck J, Muruganandam G, Sobott F, Charlier D, Loris R

R_g^Guinier	3.2	nm
D_max	10.0	nm
Volume^Porod	140	nm³

SASDPL3 – Vibrio cholerae ParD2:ParE2 complex bound to 31-bp DNA operator box

Antitoxin ParDToxin31-bp DNA operator box experimental SAS data

Sample:	Antitoxin ParD hexamer, 54 kDa Vibrio cholerae serotype … protein Toxin, 25 kDa Vibrio cholerae serotype … protein 31-bp DNA operator box monomer, 19 kDa Vibrio cholerae O1 DNA
Buffer:	20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH: 8
Experiment:	SAXS data collected at SWING, SOLEIL on 2019 Dec 4

R_g^Guinier	3.3	nm
D_max	10.5	nm
Volume^Porod	160	nm³

SASDPM3 – Vibrio cholerae ParD2:ParE2 complex bound to 33-bp DNA operator fragment

Antitoxin ParDToxin33-bp DNA operator fragment experimental SAS data

Sample:	Antitoxin ParD hexamer, 54 kDa Vibrio cholerae serotype … protein Toxin, 25 kDa Vibrio cholerae serotype … protein 33-bp DNA operator fragment monomer, 20 kDa Vibrio cholerae O1 DNA
Buffer:	20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH: 8
Experiment:	SAXS data collected at SWING, SOLEIL on 2020 Jul 18

R_g^Guinier	3.2	nm
D_max	10.0	nm
Volume^Porod	150	nm³

SASDRC8 – Human tRNA guanine transglycosylase bound to aspartate transfer RNA (tRNA-Asp)

Queuine tRNA-ribosyltransferase catalytic subunit 1Queuine tRNA-ribosyltransferase accessory subunit 2transfer RNA (Aspartate) experimental SAS data

Human tRNA guanine transglycosylase bound to aspartate transfer RNA (tRNA-Asp) Rg histogram

Sample:	Queuine tRNA-ribosyltransferase catalytic subunit 1 monomer, 44 kDa Homo sapiens protein Queuine tRNA-ribosyltransferase accessory subunit 2 monomer, 47 kDa Homo sapiens protein Transfer RNA (Aspartate) monomer, 25 kDa Homo sapiens RNA
Buffer:	20 mM HEPES, 100 mM NaCl, 3% (w/v) glycerol, pH: 7.5
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2022 Dec 1

Structural and functional investigation of tRNA guanine transglycosylase University of Göttingen Dissertation - (2023)
Katharina Sievers

R_g^Guinier	3.5	nm
D_max	10.9	nm
Volume^Porod	160	nm³

SASDR83 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA Stem loop 2 and 3 of SARS-CoV-2 in HEPES conditions

Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2Nucleoprotein experimental SAS data

Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2 Nucleoprotein Kratky plot

Sample:	Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA Nucleoprotein dimer, 30 kDa Severe acute respiratory … protein
Buffer:	25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements
Karthikeyan Dhamotharan

R_g^Guinier	2.9	nm
D_max	10.5	nm
Volume^Porod	69	nm³

SASDR93 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA Stem loop 4 with AU extension of SARS-CoV-2 in HEPES conditions

NucleoproteinStem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2 experimental SAS data

Nucleoprotein Stem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2 Kratky plot

Sample:	Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein Stem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 22 kDa Severe acute respiratory … RNA
Buffer:	25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements
Karthikeyan Dhamotharan

R_g^Guinier	3.2	nm
D_max	11.8	nm
Volume^Porod	50	nm³

SASDRA3 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA AU extension of SARS-CoV-2 in HEPES conditions

AU extension in the 5'-genomic end of SARS-CoV-2Nucleoprotein experimental SAS data

AU extension in the 5'-genomic end of SARS-CoV-2 Nucleoprotein Kratky plot

Sample:	AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 7 kDa Severe acute respiratory … RNA Nucleoprotein dimer, 30 kDa Severe acute respiratory … protein
Buffer:	25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements
Karthikeyan Dhamotharan

R_g^Guinier	2.6	nm
D_max	9.0	nm
Volume^Porod	46	nm³

SASDRB3 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA Stem loop 4 of SARS-CoV-2 in HEPES conditions

NucleoproteinStem loop 4 in the 5'-genomic end of SARS-CoV-2 experimental SAS data

Nucleoprotein Stem loop 4 in the 5'-genomic end of SARS-CoV-2 Kratky plot

Sample:	Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein Stem loop 4 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA
Buffer:	25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements
Karthikeyan Dhamotharan

R_g^Guinier	2.7	nm
D_max	10.0	nm
Volume^Porod	46	nm³

SASDS97 – polymerase alpha-primase polΔcat-prim bound to DNA in the presence of RNA initiation factors

DNA polymerase alpha subunit BDNA polymerase alpha catalytic subunitDNA primase large subunitDNA primase small subunit22mer DNA template experimental SAS data

Sample:	DNA polymerase alpha subunit B monomer, 49 kDa Homo sapiens protein DNA polymerase alpha catalytic subunit monomer, 23 kDa Homo sapiens protein DNA primase large subunit monomer, 59 kDa Homo sapiens protein DNA primase small subunit monomer, 50 kDa Homo sapiens protein 22mer DNA template monomer, 7 kDa DNA
Buffer:	20 mM HEPES, 150 mM NaCl, 5 mM MnCl2, 1 mM TCEP, 1 mM 5'-guanylylmethylenediphosphonate (GMPCPP), pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Dec 4

Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase Journal of Molecular Biology :168330 (2023)
Cordoba J, Mullins E, Salay L, Eichman B, Chazin W

R_g^Guinier	4.6	nm
D_max	14.2	nm
Volume^Porod	310	nm³

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