SAXSdb — 9pyz

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1. Structure Basics

entry_id	9pyz
deposition_date	2025-08-08
last_revision	2025-09-17
title	SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP
keywords	RNA-dependent RNA polymerase (RdRp), Viral RNA synthesis, arabinose UTP, Uridine triphosphate, nsp7, nsp8, nsp12, VIRAL PROTEIN; 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	42.35 Å
rg_electron	41.81 Å
i0	535340000.00
molecular_weight	174330.0 kDa
excluded_volume	211830 Å³
envelope_volume	303650 Å³
shell_volume	62496 Å³
envelope_diameter	160.7 Å
shell_rg	44.91 Å
envelope_rg	42.64 Å
shape_rg	41.80 Å
total_rg	42.00 Å
total_atoms	12145
n_residues	1426
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	149.2 Å
rg_real	42.53 Å
rg_real_error	1.42 Å
i0_real	5.3530e+08
i0_real_error	8.6210e+06
rg_reciprocal	42.35 Å
i0_reciprocal	535200000.0000
total_estimate	0.8560
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.4 Å
skewness	0.498
kurtosis	-0.115
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	97970000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.838

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	RNA-directed RNA polymerase nsp12
formula_weight	110424.9 kDa
ec_number	2.7.7.48,2.7.7.50
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	12145

MGSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQENLYFQGSWSHPQFEKGGSGSSWSHPQFEK

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Non-structural protein 8
formula_weight	21960.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

GAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ

Source

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

Entity 3 polymer

description	Non-structural protein 7
formula_weight	9305.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQ

Source

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

Entity 4 polymer

description	Primer RNA
formula_weight	9487.7 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	P

CAUUCUCCUAAGAAGCUAUUAAAAUCACAU

Entity 5 polymer

description	Template RNA
formula_weight	12088.1 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	T

UUUUCCCAAUGUGAUUUUAAUAGCUUCUUAGGAGAAUG

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	;URIDINE 5'-TRIPHOSPHATE ;
formula_weight	484.1 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	3.10 Å
resolution_method	—
num_particles	775227

fit	/app/data/saxs_computation/py/9pyz/9pyz.fit
pddf	/app/data/pr_computation/py/9pyz/9pyz.pr.out
profile	/app/data/saxs_computation/py/9pyz/9pyz.dat

SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)