4oq8

Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral constraints

Method: X-RAY DIFFRACTION

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

Coat protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 60 RNA 180	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 60 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 60 ;RNA (5'-R(PUPU)-3') ; × 60 PHOSPHATE ION × 60 SULFATE ION × 120 MAGNESIUM ION × 60 water × 240	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 3	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 1 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 1 ;RNA (5'-R(PUPU)-3') ; × 1 PHOSPHATE ION × 1 SULFATE ION × 2 MAGNESIUM ION × 1 water × 4	Consistent with all polymers
3	Protein–RNA	Homooligomer	Protein 5 RNA 15	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 5 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 5 ;RNA (5'-R(PUPU)-3') ; × 5 PHOSPHATE ION × 5 SULFATE ION × 10 MAGNESIUM ION × 5 water × 20	Consistent with all polymers
4	Protein–RNA	Homooligomer	Protein 6 RNA 18	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 6 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 6 ;RNA (5'-R(PUPU)-3') ; × 6 PHOSPHATE ION × 6 SULFATE ION × 12 MAGNESIUM ION × 6 water × 24	Consistent with all polymers
5	Protein–RNA	Monomer	Protein 1 RNA 3	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 1 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 1 ;RNA (5'-R(PUPU)-3') ; × 1 PHOSPHATE ION × 1 SULFATE ION × 2 MAGNESIUM ION × 1 water × 4	Consistent with all polymers
6	Protein–RNA	Homooligomer	Protein 15 RNA 45	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ; × 15 ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 15 ;RNA (5'-R(PUPU)-3') ; × 15 PHOSPHATE ION × 15 SULFATE ION × 30 MAGNESIUM ION × 15 water × 60	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COAT_STMV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 1–159

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	4oq8
Deposition date deposition_date	2014-02-07
Structure title title	Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral constraints
Keywords keywords	Double-helix RNA, Protein-RNA complex, Swiss Jelly-roll beta barrel, VIRUS-RNA complex; VIRUS/RNA
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.

4oq8__assembly_1__model_1

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

Download this curve (.dat)

4oq8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4oq8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	67.04 Å
Rg (electron density)	68.65 Å
Total Rg	68.51 Å
Atom count	93264
Residues	9840
Excluded volume	1561200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4oq8__assembly_1__model_1`	240-meric （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4oq8__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`4oq8__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`4oq8__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`4oq8__assembly_5__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`4oq8__assembly_6__model_1`	60-meric （60）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Coat protein
Molecular weight formula_weight	17533.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1946

MGRGKVKPNRKSTGDNSNVVTMIRAGSYPKVNPTPTWVRAIPFEVSVQSGIAFKVPVGSLFSANFRTDSFTSVTVMSVRAWTQLTPPVNEYSFVRLKPLFKTGDSTEEFEGRASNINTRASVGYRIPTNLRQNTVAADNVCEVRSNCRQVALVISCCFN

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PAPAPAPAPAPAPAPAPAPA)-3') ;
Molecular weight formula_weight	3247.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

AAAAAAAAAA

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ;
Molecular weight formula_weight	3016.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

UUUUUUUUUU

Entity 4 Entity 4 polymer

Description description	;RNA (5'-R(PUPU)-3') ;
Molecular weight formula_weight	567.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	277

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4oq8a_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.7 — Satellite viruses
Family Family family	b.121.7.1 — Satellite viruses

CATH v4.4 (1 domains)

Domain ID domain_id	4oq8A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

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7. Citations (8)

Satellite tobacco mosaic virus refined to 1.4 angstrom resolution.

Acta Crystallogr.,Sect.D (2014)

PMID: 25195746 · DOI: 10.1107/S1399004714013789 PRIMARY

A model for the structure of satellite tobacco mosaic virus.

J.Struct.Biol. (2012)

PMID: 22750417 · DOI: 10.1016/j.jsb.2012.06.008

Satellite tobacco mosaic virus RNA: structure and implications for assembly.

Curr.Opin.Struct.Biol. (2001)

PMID: 11179893

Refined structure of satellite tobacco mosaic virus at 1.8 A resolution.

J.Mol.Biol. (1998)

PMID: 9514737 · DOI: 10.1006/jmbi.1997.1570

Three-dimensional structure of satellite tobacco mosaic virus at 2.9 A resolution.

J.Mol.Biol. (1993)

PMID: 8510153 · DOI: 10.1006/jmbi.1993.1289

Double-helical RNA in satellite tobacco mosaic virus.

Nature (1993)

PMID: 8421525 · DOI: 10.1038/361179a0

Macromolecular crystal growth experiments on International Microgravity Laboratory--1.

Protein Sci. (1992)

PMID: 1303744 · DOI: 10.1002/pro.5560011004

Preliminary analysis of crystals of satellite tobacco mosaic virus.

J.Mol.Biol. (1989)

PMID: 2585487

Unit-cell length a length_a	172.690 Å
Unit-cell length b length_b	190.300 Å
Unit-cell length c length_c	201.690 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	120

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	48.350 Å
R factor r_factor	0.2784
R_work r_work	0.2776
R_free r_free	0.2793

Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral constraints

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

Coat 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

4oq8__assembly_1__model_1

4oq8__assembly_1__model_1 | I(q)

4oq8__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (8)

Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral constraints

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

Coat 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

4oq8__assembly_1__model_1

4oq8__assembly_1__model_1 | I(q)

4oq8__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (8)