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9uht

SARS-CoV-2 E-RTC in complex with RNA-nsp9 and GMPPNP

Method: ELECTRON MICROSCOPY D_max: 176.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uht
deposition_date	2025-04-14
title	SARS-CoV-2 E-RTC in complex with RNA-nsp9 and GMPPNP
keywords	SARS-COV-2, CAPPING, CRYO-EM, PROTEIN, VIRAL PROTEIN/RNA, VIRAL PROTEIN-RNA complex; VIRAL PROTEIN/RNA
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	52.77 Å
rg_electron	52.82 Å
i0	1561960000.00
molecular_weight	315660.0 kDa
excluded_volume	388990 Å³
envelope_volume	593660 Å³
shell_volume	95510 Å³
envelope_diameter	177.7 Å
shell_rg	55.14 Å
envelope_rg	51.15 Å
shape_rg	52.86 Å
total_rg	52.75 Å
total_atoms	22051
n_residues	2727
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	176.8 Å
rg_real	52.66 Å
rg_real_error	1.49 Å
i0_real	1.5620e+09
i0_real_error	3.1780e+07
rg_reciprocal	52.85 Å
i0_reciprocal	1562000000.0000
total_estimate	0.8872
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.8 Å
skewness	0.191
kurtosis	-0.477
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0001
highest_alpha	101700000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.872

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	RNA-directed RNA polymerase nsp12
formula_weight	106781.0 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	22068

SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQ

Source

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

Entity 2 polymer

description	Non-structural protein 8
formula_weight	21903.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ

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	8678.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDN

Source

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

Entity 4 polymer

description	Helicase nsp13
formula_weight	65989.4 kDa
ec_number	3.6.4.12,3.6.4.13
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIP

Source

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

Entity 5 polymer

description	Viral protein genome-linked nsp9
formula_weight	12391.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

NNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ

Source

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

Entity 6 polymer

description	;RNA (5'-R(PAPUPUPA)-3') ;
formula_weight	1225.8 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	H

AUUA

Source

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

Entity 7 polymer

description	PRIMER
formula_weight	8172.9 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	I

GCGGUAGUAGCAUGCUAGGGAGCAG

Source

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

Entity 8 polymer

description	TEMPLATE
formula_weight	8522.1 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	J

UGACUGCUCCCUAGCAUGCUACUACCG

Source

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

Entity 9 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	8

Entity 10 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
formula_weight	522.2 kDa
src_method	syn
entity_count	1

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

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6. Citations (1)

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resolution	2.890 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

fit	/app/data/saxs_computation/uh/9uht/9uht.fit
pddf	/app/data/pr_computation/uh/9uht/9uht.pr.out
profile	/app/data/saxs_computation/uh/9uht/9uht.dat

SARS-CoV-2 E-RTC in complex with RNA-nsp9 and GMPPNP

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)