SAXSdb — 9prc

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

Small delta antigen

Hepatitis delta virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 8 RNA 4	Palindromic RNA × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SHDAG_HDVD3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–194； UniProt 2–195 Author chain B； PDBConstruct 1–194； UniProt 2–195 Author chain C； PDBConstruct 1–194； UniProt 2–195 Author chain D； PDBConstruct 1–194； UniProt 2–195 Author chain E； PDBConstruct 1–194； UniProt 2–195 Author chain F； PDBConstruct 1–194； UniProt 2–195 Author chain G； PDBConstruct 1–194； UniProt 2–195 Author chain H； PDBConstruct 1–194； UniProt 2–195

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	9prc
Deposition date deposition_date	2025-07-23
Structure title title	HDAg complex with 86-pRNA, Body1
Keywords keywords	HDV, HDAg, RNP, RNA, VIRUS; VIRUS
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.

9prc__assembly_1__model_1

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

Download this curve (.dat)

9prc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9prc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.36 Å
Rg (electron density)	38.30 Å
Total Rg	38.65 Å
Atom count	6493
Residues	553
Excluded volume	104970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9prc__assembly_1__model_1`	dodecameric （12）	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 (2)

Entity 1 Entity 1 polymer

Description description	Small delta antigen
Molecular weight formula_weight	21854.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	6493

SRPEGRKNRGGREEVLEQWVSGRKKLEELERDLRKVKKKIKKLEDEHPWLGNIKGILGKKDKDGEGAPPAKRARTDQMEVDSGPRKRPSRGGFTDKERQDHRRRKALENKRKQLSAGGKNLSKEEEEELRRLTEEDERRERRIAGPQVGGVNPLEGGTRGAPGGGFVPSMQGVPESPFTRTGEGLDIRGSQGFP

Source Source

Source organism organism	Hepatitis delta virus
NCBI taxonomy ID ncbi_taxonomy_id	12475
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Palindromic RNA
Molecular weight formula_weight	17581.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	J,K,M,P

GGGAGAAUAUAUAUAUAUAUAUAUAUGUUUAUAUAUAUAUAUAUAUAUAUGAAUU

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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	3.500 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	298422

HDAg complex with 86-pRNA, Body1

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

Small delta antigen

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

9prc__assembly_1__model_1

9prc__assembly_1__model_1 | I(q)

9prc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Citations (1)

HDAg complex with 86-pRNA, Body1

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

Small delta antigen

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

9prc__assembly_1__model_1

9prc__assembly_1__model_1 | I(q)

9prc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Citations (1)