SAXSdb — 9sao

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1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA-directed RNA polymerase nsp12

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 3 RNA 2	RNA primer strand (25-MER) × 1 RNA template strand (40-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R1AB_SARS2
Isoform	—
PDB entities	3, 4, 5
Chains and sequence ranges	Author chain A； PDBConstruct 1–928； UniProt 4397–5324 Author chain B； PDBConstruct 1–198； UniProt 3943–4140 Author chain C； PDBConstruct 1–83； UniProt 3860–3942

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9sao
Deposition date deposition_date	2025-08-07
Last revision last_revision	2025-10-01
Structure title title	Cryo-EM structure of SARS CoV-2 RdRp S759A mutant in complex with 20-40mer RNA incorporating remdesivir
Keywords keywords	RNA-dependent RNA polymerase, SARS CoV-2, transcription, viral protein, ATP, remdesivir, S759A mutant; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9sao__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9sao__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9sao__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.27 Å
Rg (electron density)	31.42 Å
Total Rg	32.05 Å
Atom count	8697
Residues	1036
Excluded volume	153060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9sao__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	RNA primer strand (25-MER)
Molecular weight formula_weight	8000.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	P
Atom count atom_count	8697

GUCAUUCUCCUAAGAAGCUAUUXXX

Entity 2 Entity 2 polymer

Description description	RNA template strand (40-MER)
Molecular weight formula_weight	12720.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	T

CUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC

Entity 3 Entity 3 polymer

Description description	RNA-directed RNA polymerase nsp12
Molecular weight formula_weight	106420.6 kDa
EC 编号 ec_number	2.7.7.48,2.7.7.50
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

QSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILADDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQ

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Non-structural protein 8
Molecular weight formula_weight	21903.0 kDa
EC 编号 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.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Non-structural protein 7
Molecular weight formula_weight	9248.8 kDa
EC 编号 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.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQ

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	167051

Cryo-EM structure of SARS CoV-2 RdRp S759A mutant in complex with 20-40mer RNA incorporating remdesivir

1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA-directed RNA polymerase nsp12

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9sao__assembly_1__model_1

9sao__assembly_1__model_1 | I(q)

9sao__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

7. Citations (1)

Cryo-EM structure of SARS CoV-2 RdRp S759A mutant in complex with 20-40mer RNA incorporating remdesivir

1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA-directed RNA polymerase nsp12

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9sao__assembly_1__model_1

9sao__assembly_1__model_1 | I(q)

9sao__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

7. Citations (1)