SAXSdb — 9sap

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1. Structure Basics

entry_id	9sap
deposition_date	2025-08-07
last_revision	2025-10-01
title	Cryo-EM structure of SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporating Remdesivir
keywords	RNA-dependent RNA polymerase, SARS CoV-2, transcription, viral protein, ATP, remdesivir, S759A mutant; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	32.07 Å
rg_electron	31.25 Å
i0	260526000.00
molecular_weight	123810.0 kDa
excluded_volume	152470 Å³
envelope_volume	196100 Å³
shell_volume	50232 Å³
envelope_diameter	110.0 Å
shell_rg	39.90 Å
envelope_rg	31.24 Å
shape_rg	31.26 Å
total_rg	31.88 Å
total_atoms	8663
n_residues	1032
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	106.5 Å
rg_real	31.89 Å
rg_real_error	0.63 Å
i0_real	2.6050e+08
i0_real_error	3.8330e+06
rg_reciprocal	31.97 Å
i0_reciprocal	260500000.0000
total_estimate	0.8836
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.1 Å
skewness	0.182
kurtosis	-0.451
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	60000000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	RNA primer strand (25-MER)
formula_weight	8000.8 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	P
atom_count	8663

GUCAUUCUCCUAAGAAGCUAUUXXX

Entity 2 polymer

description	RNA template strand (40-MER)
formula_weight	12720.5 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	T

CUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC

Entity 3 polymer

description	RNA-directed RNA polymerase nsp12
formula_weight	106436.6 kDa
ec_number	2.7.7.48,2.7.7.50
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

QSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	Non-structural protein 8
formula_weight	21903.0 kDa
ec_number	3.4.19.12,3.4.22.-,3.4.22.69,2.7.7.48,3.6.4.12,3.6.4.13,3.1.13.-,3.1.-.-,2.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

description	Non-structural protein 7
formula_weight	9248.8 kDa
ec_number	3.4.19.12,3.4.22.-,3.4.22.69,2.7.7.48,3.6.4.12,3.6.4.13,3.1.13.-,3.1.-.-,2.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.90 Å
resolution_method	—
num_particles	145169

fit	/app/data/saxs_computation/sa/9sap/9sap.fit
pddf	/app/data/pr_computation/sa/9sap/9sap.pr.out
profile	/app/data/saxs_computation/sa/9sap/9sap.dat

Cryo-EM structure of SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporating Remdesivir

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)