SAXSdb — 8zfv

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

Nucleoprotein

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 homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 Ceftriaxone × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	Ceftriaxone × 1 DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCAP_SARS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–175； UniProt 247–419 Author chain B； PDBConstruct 3–175； UniProt 247–419 Author chain C； PDBConstruct 3–175； UniProt 247–419 Author chain D； PDBConstruct 3–175； UniProt 247–419

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	8zfv
Deposition date deposition_date	2024-05-08
Last revision last_revision	2025-04-02
Structure title title	Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone
Keywords keywords	SARS-CoV-2, Nucleocapsid protein, RNA binding C-terminal domain, drugs, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

8zfv__assembly_1__model_1

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

Download this curve (.dat)

8zfv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8zfv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.79 Å
Rg (electron density)	18.52 Å
Total Rg	19.61 Å
Atom count	1875
Residues	226
Excluded volume	32889 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8zfv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8zfv__assembly_2__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	Nucleoprotein
Molecular weight formula_weight	19569.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,B,D
Atom count atom_count	4417

MGTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA

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 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	Ceftriaxone
Molecular weight formula_weight	554.6 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	669

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Unit-cell length a length_a	43.539 Å
Unit-cell length b length_b	46.643 Å
Unit-cell length c length_c	69.021 Å
Unit-cell angle α angle_alpha	106.66 °
Unit-cell angle β angle_beta	90.11 °
Unit-cell angle γ angle_gamma	93.46 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	26.580 Å
R factor r_factor	0.1502
R_work r_work	0.1473
R_free r_free	0.2049

Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone

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

Nucleoprotein

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

8zfv__assembly_1__model_1

8zfv__assembly_1__model_1 | I(q)

8zfv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone

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

Nucleoprotein

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

8zfv__assembly_1__model_1

8zfv__assembly_1__model_1 | I(q)

8zfv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)