SAXSdb — 9rp8

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

Capsid protein

Turnip crinkle virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E7E1K6_TCV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–351； UniProt 1–351 Author chain B； PDBConstruct 1–351； UniProt 1–351 Author chain C； PDBConstruct 1–351； UniProt 1–351 Author chain D； PDBConstruct 1–351； UniProt 1–351 Author chain E； PDBConstruct 1–351； UniProt 1–351 Author chain F； PDBConstruct 1–351； UniProt 1–351 Author chain G； PDBConstruct 1–351； UniProt 1–351 Author chain H； PDBConstruct 1–351； UniProt 1–351 Author chain I； PDBConstruct 1–351； UniProt 1–351 Author chain J； PDBConstruct 1–351； UniProt 1–351 Author chain K； PDBConstruct 1–351； UniProt 1–351 Author chain L； PDBConstruct 1–351； UniProt 1–351 Author chain M； PDBConstruct 1–351； UniProt 1–351 Author chain N； PDBConstruct 1–351； UniProt 1–351 Author chain O； PDBConstruct 1–351； UniProt 1–351 Author chain P； PDBConstruct 1–351； UniProt 1–351 Author chain Q； PDBConstruct 1–351； UniProt 1–351 Author chain R； PDBConstruct 1–351； UniProt 1–351 Author chain S； PDBConstruct 1–351； UniProt 1–351 Author chain T； PDBConstruct 1–351； UniProt 1–351

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	9rp8
Deposition date deposition_date	2025-06-24
Last revision last_revision	2026-06-03
Structure title title	Crystal structure of the T=1 icosahedral capsid of Turnip Crinkle Virus P38
Keywords keywords	plant viral suppressor, RNA silencing, VSR, RNAi, janus head, T=1 icosahedral symmetry, capsid, virus-like particle, 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.

9rp8__assembly_1__model_1

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

Download this curve (.dat)

9rp8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9rp8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	87.12 Å
Rg (electron density)	86.09 Å
Total Rg	86.15 Å
Atom count	124071
Residues	16320
Excluded volume	2194800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rp8__assembly_1__model_1`	60-meric （60）	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 (1)

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Unit-cell length a length_a	203.383 Å
Unit-cell length b length_b	203.383 Å
Unit-cell length c length_c	469.128 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	180

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	trigonal

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	48.810 Å
R factor r_factor	0.1986
R_work r_work	0.1735
R_free r_free	0.1932

Description description	Capsid protein
Molecular weight formula_weight	38185.0 kDa
Source method src_method	man
Copy count entity_count	20

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,N,M,L,P,O,T,S,R,Q
Atom count atom_count	41357

Crystal structure of the T=1 icosahedral capsid of Turnip Crinkle Virus P38

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

Capsid protein

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

9rp8__assembly_1__model_1

9rp8__assembly_1__model_1 | I(q)

9rp8__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Source organism organism	Turnip crinkle virus
NCBI taxonomy ID ncbi_taxonomy_id	11988
Host organism host_organism	Escherichia coli K-12

Crystal structure of the T=1 icosahedral capsid of Turnip Crinkle Virus P38

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

Capsid protein

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

9rp8__assembly_1__model_1

9rp8__assembly_1__model_1 | I(q)

9rp8__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)