Small Angle Scattering Biological Data Bank SASBDB

MACROMOLECULE TYPE: heterocomplex

SASDSA7 – polymerase alpha-primase polΔcat-prim bound to DNA in the presence of an RNA-primed template

DNA polymerase alpha subunit BDNA polymerase alpha catalytic subunitDNA primase large subunitDNA primase small subunit29 mer DNA template8mer RNA primer 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 29 mer DNA template monomer, 9 kDa DNA 8mer RNA primer monomer, 3 kDa RNA
Buffer:	20 mM HEPES, 150 mM NaCl, 5 mM MgCl2, 1 mM TCEP, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2023 Mar 28

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	4.9	nm
D_max	15.3	nm
Volume^Porod	344	nm³

SASDM63 – RRM1-ZnF1-RRM2 triple domains of RNA-binding protein 5 (C191G mutant) in complex with GGCU_12 RNA

RNA Binding Motif protein 5 (I107T, C191G)Caspase-2 derived RNA GGCU_12 experimental SAS data

Sample:	RNA Binding Motif protein 5 (I107T, C191G) monomer, 26 kDa Homo sapiens protein Caspase-2 derived RNA GGCU_12 monomer, 4 kDa RNA
Buffer:	20 mM MES, 100 mM NaCl, 1 mM DTT, pH: 6.5
Experiment:	SAXS data collected at Rigaku BioSAXS-1000, SFB 1035, Technische Universität München on 2017 Mar 1

Structural basis for specific RNA recognition by the alternative splicing factor RBM5. Nat Commun 14(1):4233 (2023)
Soni K, Jagtap PKA, Martínez-Lumbreras S, Bonnal S, Geerlof A, Stehle R, Simon B, Valcárcel J, Sattler M

R_g^Guinier	2.2	nm
D_max	7.5	nm
Volume^Porod	42	nm³

SASDPQ6 – 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 phosphate conditions

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

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

Sample:	Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA
Buffer:	25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2021 Aug 16

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements. Nat Commun 14(1):3331 (2023)
Korn SM, Dhamotharan K, Jeffries CM, Schlundt A

R_g^Guinier	2.4	nm
D_max	9.0	nm
Volume^Porod	38	nm³

SASDPR6 – 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 phosphate 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 potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2021 Aug 16

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements. Nat Commun 14(1):3331 (2023)
Korn SM, Dhamotharan K, Jeffries CM, Schlundt A

R_g^Guinier	3.4	nm
D_max	13.5	nm
Volume^Porod	51	nm³

SASDPS6 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA AU extension of SARS-CoV-2 in phosphate conditions

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

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

Sample:	Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 7 kDa Severe acute respiratory … RNA
Buffer:	25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2021 Aug 16

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements. Nat Commun 14(1):3331 (2023)
Korn SM, Dhamotharan K, Jeffries CM, Schlundt A

R_g^Guinier	2.1	nm
D_max	8.5	nm
Volume^Porod	32	nm³

SASDPT6 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) with 5'-genomic RNA Stem loop 4 of SARS-CoV-2 in phosphate conditions (mixture)

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 potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2021 Nov 22

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements. Nat Commun 14(1):3331 (2023)
Korn SM, Dhamotharan K, Jeffries CM, Schlundt A

R_g^Guinier	2.1	nm
D_max	7.8	nm
Volume^Porod	25	nm³

SASDPZ5 – Gcf1p protein bound to DNA at 1.0 mg/mL

Sample:	Gcf1p monomer, 26 kDa Candida albicans (strain … protein Af2_20 DNA monomer, 12 kDa DNA
Buffer:	25 mM Tris, 20 mM NaCl, pH: 8
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2019 Aug 30

Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism. Nucleic Acids Res (2023)
Tarrés-Solé A, Battistini F, Gerhold JM, Piétrement O, Martínez-García B, Ruiz-López E, Lyonnais S, Bernadó P, Roca J, Orozco M, Le Cam E, Sedman J, Solà M

R_g^Guinier	3.6	nm
D_max	16.0	nm
Volume^Porod	92	nm³

SASDP26 – Gcf1p protein bound to DNA at 2.0 mg/mL

Sample:	Gcf1p monomer, 26 kDa Candida albicans (strain … protein Af2_20 DNA monomer, 12 kDa DNA
Buffer:	25 mM Tris, 20 mM NaCl, pH: 8
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2019 Aug 30

R_g^Guinier	3.9	nm
D_max	16.0	nm
Volume^Porod	133	nm³

SASDP36 – N-terminal truncated Gcf1p (amino acids 59-245) bound to DNA

Af2_20 DNAGcf1p(Δ58) experimental SAS data

Sample:	Af2_20 DNA monomer, 12 kDa DNA Gcf1p(Δ58) monomer, 22 kDa Candida albicans (strain … protein
Buffer:	25 mM Tris, 20 mM NaCl, pH: 8
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2019 Aug 30

R_g^Guinier	2.6	nm
D_max	10.5	nm
Volume^Porod	52	nm³

SASDR94 – GAC rRNA + L11 Protein: Time-Resolved 30 ms

58 nucleotide RNA L11-binding domain from E. coli 23S rRNA50S ribosomal protein L11 experimental SAS data

58 nucleotide RNA L11-binding domain from E. coli 23S rRNA 50S ribosomal protein L11 Kratky plot

Sample:	58 nucleotide RNA L11-binding domain from E. coli 23S rRNA monomer, 19 kDa Escherichia coli RNA 50S ribosomal protein L11 monomer, 16 kDa Thermus thermophilus protein
Buffer:	10 mM Na-MOPSO, 100 mM KCl, pH: 6.5
Experiment:	SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2018 May 9

Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering IUCrJ 10(3):363-375 (2023)
Zielinski K, Katz A, Calvey G, Pabit S, Milano S, Aplin C, San Emeterio J, Cerione R, Pollack L

R_g^Guinier	2.4	nm
D_max	12.0	nm
Volume^Porod	34	nm³

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