Small Angle Scattering Biological Data Bank SASBDB

SASBDB entries for UniProt ID:

SASDJA4 – Endonuclease VIII from E. coli (size exclusion chromatography SAXS)

UniProt ID: P50465 (2-263) Endonuclease 8

Sample:	Endonuclease 8 monomer, 31 kDa Escherichia coli protein
Buffer:	25 mM Bis-Tris, 150 mM NaCl, 2% glycerol, 1 mM TCEP, pH: 8
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Mar 9

Unique Structural Features of Mammalian NEIL2 DNA Glycosylase Prime Its Activity for Diverse DNA Substrates and Environments. Structure (2020)
Eckenroth BE, Cao VB, Averill AM, Dragon JA, Doublié S

R_g^Guinier	2.3	nm
D_max	7.8	nm
Volume^Porod	45	nm³

SASDJB4 – Endonuclease VIII - Like 2 from Monodelphis domestica (size exclusion chromatography SAXS) full length

UniProt ID: F7AMK3 (3-336) Nei like DNA glycosylase 2

Nei like DNA glycosylase 2 experimental SAS data

Sample:	Nei like DNA glycosylase 2 monomer, 39 kDa Monodelphis domestica protein
Buffer:	25 mM Bis-Tris, 150 mM NaCl, 2% glycerol, 1 mM TCEP, pH: 8
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Mar 9

R_g^Guinier	2.7	nm
D_max	8.2	nm
Volume^Porod	58	nm³

SASDJC4 – Endonuclease VIII - Like 2 from Monodelphis domestica (size exclusion chromatography SAXS) MdoNEIL2 cut (Δ67-133)

UniProt ID: F7AMK3 (None-None) Nei like DNA glycosylase 2 (Δ67-133)

Nei like DNA glycosylase 2 (Δ67-133) experimental SAS data

Sample:	Nei like DNA glycosylase 2 (Δ67-133) monomer, 33 kDa Monodelphis domestica protein
Buffer:	25 mM Bis-Tris, 150 mM NaCl, 2% glycerol, 1 mM TCEP, pH: 8
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Mar 9

R_g^Guinier	2.4	nm
D_max	7.8	nm
Volume^Porod	47	nm³

SASDJD4 – Bacteriorhodopsin solubilized in contrast-matched octyl glucoside

UniProt ID: P02945 (14-262) Bacteriorhodopsin

Sample:	Bacteriorhodopsin monomer, 27 kDa Halobacterium salinarum protein
Buffer:	25 mM NaH2PO4, 1.35 mM KOH, 40 mM partially-deuterated octyl glucoside mixture, pH: 5.6
Experiment:	SANS data collected at NGB 30m SANS, NIST Center for High Resolution Neutron Scattering (CHRNS) on 2017 Jan 20

Direct localization of detergents and bacteriorhodopsin in the lipidic cubic phase by small-angle neutron scattering IUCrJ 8(1) (2021)
Cleveland IV T, Blick E, Krueger S, Leung A, Darwish T, Butler P

R_g^Guinier	2.7	nm
D_max	5.4	nm
Volume^Porod	68	nm³

SASDJE4 – Bacteriorhodopsin in contrast-matched lipidic cubic phase formed with deuterated monoolein

UniProt ID: P02945 (14-262) Bacteriorhodopsin

Sample:	Bacteriorhodopsin monomer, 27 kDa Halobacterium salinarum protein
Buffer:	25 mM NaH2PO4, 1.35 mM KOH, 40 mM octyl glucoside, pH: 5.6
Experiment:	SANS data collected at NG7, NIST Center for High Resolution Neutron Scattering (CHRNS) on 2017 May 15

R_g^Guinier	2.7	nm
D_max	6.2	nm
Volume^Porod	49	nm³

SASDJG4 – SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD)

UniProt ID: P0DTC2 (319-566) Spike glycoprotein (ACE2 receptor binding domain)

Spike glycoprotein (ACE2 receptor binding domain) experimental SAS data

Sample:	Spike glycoprotein (ACE2 receptor binding domain) monomer, 29 kDa Severe acute respiratory … protein
Buffer:	25 mM Tris 100 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2020 May 1

Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2 Nature Communications 11(1) (2020)
Custódio T, Das H, Sheward D, Hanke L, Pazicky S, Pieprzyk J, Sorgenfrei M, Schroer M, Gruzinov A, Jeffries C, Graewert M, Svergun D, Dobrev N, Remans K, Seeger M, McInerney G, Murrell B, Hällberg B, Löw C

R_g^Guinier	3.0	nm
D_max	13.1	nm
Volume^Porod	64	nm³

SASDJH4 – SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23)

UniProt ID: None (None-None) Synthetic nanobody Sybody 23

UniProt ID: P0DTC2 (319-566) Spike glycoprotein (ACE2 receptor binding domain)

Synthetic nanobody Sybody 23Spike glycoprotein (ACE2 receptor binding domain) experimental SAS data

Sample:	Synthetic nanobody Sybody 23 monomer, 16 kDa synthetic construct protein Spike glycoprotein (ACE2 receptor binding domain) monomer, 29 kDa Severe acute respiratory … protein
Buffer:	25 mM Tris 100 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at EMBL P12, PETRA III on 2020 May 10

R_g^Guinier	3.5	nm
D_max	15.1	nm
Volume^Porod	87	nm³

SASDJK4 – RNA polymerase core complex

UniProt ID: P9WGZ1 (1-347) DNA-directed RNA polymerase subunit alpha

UniProt ID: P9WGY9 (7-1178) DNA-directed RNA polymerase subunit beta

UniProt ID: P9WGY7 (2-1316) DNA-directed RNA polymerase subunit beta'

UniProt ID: P9WGY5 (2-110) DNA-directed RNA polymerase subunit omega

DNA-directed RNA polymerase subunit alphaDNA-directed RNA polymerase subunit betaDNA-directed RNA polymerase subunit beta'DNA-directed RNA polymerase subunit omega experimental SAS data

Sample:	DNA-directed RNA polymerase subunit alpha dimer, 78 kDa Mycobacterium tuberculosis protein DNA-directed RNA polymerase subunit beta monomer, 129 kDa Mycobacterium tuberculosis protein DNA-directed RNA polymerase subunit beta' monomer, 147 kDa Mycobacterium tuberculosis protein DNA-directed RNA polymerase subunit omega monomer, 12 kDa Mycobacterium tuberculosis protein
Buffer:	10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH: 8
Experiment:	SAXS data collected at BM29, ESRF on 2018 Mar 8

Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair
Ravishankar Ramachandran

R_g^Guinier	5.1	nm
D_max	19.3	nm
Volume^Porod	262	nm³

SASDJL4 – RNA polymerase core subunit in complex with ATP-dependent DNA helicase UvrD1

UniProt ID: P9WGZ1 (1-347) DNA-directed RNA polymerase subunit alpha

UniProt ID: P9WGY9 (7-1178) DNA-directed RNA polymerase subunit beta

UniProt ID: P9WGY7 (2-1316) DNA-directed RNA polymerase subunit beta'

UniProt ID: P9WGY5 (1-110) DNA-directed RNA polymerase subunit omega

UniProt ID: P9WMQ1 (1-771) ATP-dependent DNA helicase UvrD1

Sample:	DNA-directed RNA polymerase subunit alpha dimer, 75 kDa Mycobacterium tuberculosis protein DNA-directed RNA polymerase subunit beta monomer, 129 kDa Mycobacterium tuberculosis protein DNA-directed RNA polymerase subunit beta' monomer, 147 kDa Mycobacterium tuberculosis protein DNA-directed RNA polymerase subunit omega monomer, 12 kDa Mycobacterium tuberculosis protein ATP-dependent DNA helicase UvrD1 monomer, 85 kDa Mycobacterium tuberculosis protein
Buffer:	10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH: 8
Experiment:	SAXS data collected at BM29, ESRF on 2018 Mar 11

Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair
Ravishankar Ramachandran

R_g^Guinier	7.5	nm
D_max	22.2	nm
Volume^Porod	898	nm³

SASDJM4 – ATP-dependent DNA helicase UvrD1 (Apo-UvrD)

UniProt ID: P9WMQ1 (1-771) ATP-dependent DNA helicase UvrD1

ATP-dependent DNA helicase UvrD1 experimental SAS data

Sample:	ATP-dependent DNA helicase UvrD1 monomer, 85 kDa Mycobacterium tuberculosis protein
Buffer:	10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH: 8
Experiment:	SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2020 Feb 28

Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair
Ravishankar Ramachandran

R_g^Guinier	3.4	nm
D_max	8.4	nm
Volume^Porod	132	nm³

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