SAXSdb — 8qkm

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

Capsid protein

Satellite tobacco necrosis virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	CALCIUM ION × 92	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAPSD_STNV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 0； PDBConstruct 1–188； UniProt 9–196 Author chain 1； PDBConstruct 1–188； UniProt 9–196 Author chain 2； PDBConstruct 1–188； UniProt 9–196 Author chain 3； PDBConstruct 1–188； UniProt 9–196 Author chain 4； PDBConstruct 1–188； UniProt 9–196 Author chain 5； PDBConstruct 1–188； UniProt 9–196 Author chain 6； PDBConstruct 1–188； UniProt 9–196 Author chain 7； PDBConstruct 1–188； UniProt 9–196 Author chain A； PDBConstruct 1–188； UniProt 9–196 Author chain B； PDBConstruct 1–188； UniProt 9–196 Author chain C； PDBConstruct 1–188； UniProt 9–196 Author chain D； PDBConstruct 1–188； UniProt 9–196 Author chain E； PDBConstruct 1–188； UniProt 9–196 Author chain F； PDBConstruct 1–188； UniProt 9–196 Author chain G； PDBConstruct 1–188； UniProt 9–196 Author chain H； PDBConstruct 1–188； UniProt 9–196 Author chain I； PDBConstruct 1–188； UniProt 9–196 Author chain J； PDBConstruct 1–188； UniProt 9–196 Author chain K； PDBConstruct 1–188； UniProt 9–196 Author chain L； PDBConstruct 1–188； UniProt 9–196 Author chain M； PDBConstruct 1–188； UniProt 9–196 Author chain N； PDBConstruct 1–188； UniProt 9–196 Author chain O； PDBConstruct 1–188； UniProt 9–196 Author chain P； PDBConstruct 1–188； UniProt 9–196 Author chain Q； PDBConstruct 1–188； UniProt 9–196 Author chain R； PDBConstruct 1–188； UniProt 9–196 Author chain S； PDBConstruct 1–188； UniProt 9–196 Author chain T； PDBConstruct 1–188； UniProt 9–196 Author chain U； PDBConstruct 1–188； UniProt 9–196 Author chain V； PDBConstruct 1–188； UniProt 9–196 Author chain W； PDBConstruct 1–188； UniProt 9–196 Author chain X； PDBConstruct 1–188； UniProt 9–196 Author chain Y； PDBConstruct 1–188； UniProt 9–196 Author chain Z； PDBConstruct 1–188； UniProt 9–196 Author chain a； PDBConstruct 1–188； UniProt 9–196 Author chain b； PDBConstruct 1–188； UniProt 9–196 Author chain c； PDBConstruct 1–188； UniProt 9–196 Author chain d； PDBConstruct 1–188； UniProt 9–196 Author chain e； PDBConstruct 1–188； UniProt 9–196 Author chain f； PDBConstruct 1–188； UniProt 9–196 Author chain g； PDBConstruct 1–188； UniProt 9–196 Author chain h； PDBConstruct 1–188； UniProt 9–196 Author chain i； PDBConstruct 1–188； UniProt 9–196 Author chain j； PDBConstruct 1–188； UniProt 9–196 Author chain k； PDBConstruct 1–188； UniProt 9–196 Author chain l； PDBConstruct 1–188； UniProt 9–196 Author chain m； PDBConstruct 1–188； UniProt 9–196 Author chain n； PDBConstruct 1–188； UniProt 9–196 Author chain o； PDBConstruct 1–188； UniProt 9–196 Author chain p； PDBConstruct 1–188； UniProt 9–196 Author chain q； PDBConstruct 1–188； UniProt 9–196 Author chain r； PDBConstruct 1–188； UniProt 9–196 Author chain s； PDBConstruct 1–188； UniProt 9–196 Author chain t； PDBConstruct 1–188； UniProt 9–196 Author chain u； PDBConstruct 1–188； UniProt 9–196 Author chain v； PDBConstruct 1–188； UniProt 9–196 Author chain w； PDBConstruct 1–188； UniProt 9–196 Author chain x； PDBConstruct 1–188； UniProt 9–196 Author chain y； PDBConstruct 1–188； UniProt 9–196 Author chain z； PDBConstruct 1–188； UniProt 9–196

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	8qkm
Deposition date deposition_date	2023-09-15
Structure title title	Symmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 gRNA
Keywords keywords	STNV, CryoEM, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
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.

8qkm__assembly_1__model_1

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

Download this curve (.dat)

8qkm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8qkm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	77.71 Å
Rg (electron density)	76.94 Å
Total Rg	76.93 Å
Atom count	87512
Residues	11280
Excluded volume	1552000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8qkm__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 (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	2.39 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	78988

Description description	Capsid protein
Molecular weight formula_weight	20766.5 kDa
Source method src_method	man
Copy count entity_count	60

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,0,1,2,3,4,5,6,7
Atom count atom_count	87512

Symmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 gRNA

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

8qkm__assembly_1__model_1

8qkm__assembly_1__model_1 | I(q)

8qkm__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

7. Citations (1)

Source organism organism	Satellite tobacco necrosis virus 1
NCBI taxonomy ID ncbi_taxonomy_id	12445
Host organism host_organism	Escherichia coli

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	92

Symmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 gRNA

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

8qkm__assembly_1__model_1

8qkm__assembly_1__model_1 | I(q)

8qkm__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

7. Citations (1)