4oq9

Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints

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 × 12 SULFATE ION × 72 SODIUM ION × 68 MAGNESIUM ION × 12 water × 200	Consistent with all polymers
2	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 × 3 SULFATE ION × 18 SODIUM ION × 17 MAGNESIUM ION × 3 water × 50	Consistent with all polymers
3	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 × 3 SULFATE ION × 18 SODIUM ION × 17 MAGNESIUM ION × 3 water × 50	Consistent with all polymers
4	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 × 3 SULFATE ION × 18 SODIUM ION × 17 MAGNESIUM ION × 3 water × 50	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 Author chain B； PDBConstruct 1–159； UniProt 1–159 Author chain C； PDBConstruct 1–159； UniProt 1–159 Author chain D； PDBConstruct 1–159； UniProt 1–159 Author chain E； PDBConstruct 1–159； UniProt 1–159 Author chain F； PDBConstruct 1–159； UniProt 1–159 Author chain G； PDBConstruct 1–159； UniProt 1–159 Author chain H； PDBConstruct 1–159； UniProt 1–159 Author chain I； PDBConstruct 1–159； UniProt 1–159 Author chain J； PDBConstruct 1–159； UniProt 1–159 Author chain K； PDBConstruct 1–159； UniProt 1–159 Author chain L； PDBConstruct 1–159； UniProt 1–159 Author chain M； PDBConstruct 1–159； UniProt 1–159 Author chain N； PDBConstruct 1–159； UniProt 1–159 Author chain O； 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	4oq9
Deposition date deposition_date	2014-02-07
Structure title title	Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints
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.

4oq9__assembly_1__model_1

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

Download this curve (.dat)

4oq9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4oq9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	69.42 Å
Rg (electron density)	70.49 Å
Total Rg	70.39 Å
Atom count	81280
Residues	9312
Excluded volume	1392900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4oq9__assembly_1__model_1`	240-meric （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4oq9__assembly_2__model_1`	60-meric （60）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`4oq9__assembly_3__model_1`	60-meric （60）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`4oq9__assembly_4__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 (9)

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	15

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O
Atom count atom_count	29296

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	15

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d

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	15

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	e,f,g,h,i,j,k,l,m,n,o,p,q,r,s

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	15

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	t,u,v,w,x,y,z,1,2,3,4,5,6,7,8

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	3

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	18

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4276

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d4oq9a_
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

Domain ID domain_id	d4oq9b_
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

Domain ID domain_id	d4oq9c_
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

Domain ID domain_id	d4oq9d_
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

Domain ID domain_id	d4oq9e_
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

Domain ID domain_id	d4oq9f_
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

Domain ID domain_id	d4oq9g_
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

Domain ID domain_id	d4oq9h_
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

Domain ID domain_id	d4oq9i_
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

Domain ID domain_id	d4oq9j_
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

Domain ID domain_id	d4oq9k_
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

Domain ID domain_id	d4oq9l_
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

Domain ID domain_id	d4oq9m_
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

Domain ID domain_id	d4oq9n_
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

Domain ID domain_id	d4oq9o_
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 (15 domains)

Domain ID domain_id	4oq9A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9E00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9G00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9H00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9I00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9J00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9K00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9L00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9M00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9N00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	220 — Satellite virus coat domain

Domain ID domain_id	4oq9O00
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	0.2182
R_work r_work	0.2165
R_free r_free	0.2497

Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints

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

4oq9__assembly_1__model_1

4oq9__assembly_1__model_1 | I(q)

4oq9__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 (9)

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 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

CATH v4.4 (15 domains)

7. Citations (8)

Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints

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

4oq9__assembly_1__model_1

4oq9__assembly_1__model_1 | I(q)

4oq9__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 (9)

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 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

CATH v4.4 (15 domains)

7. Citations (8)