4nia

Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS 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 MAGNESIUM ION × 12 PHOSPHATE ION × 12 SULFATE ION × 4 water × 200	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	4nia
Deposition date deposition_date	2013-11-05
Structure title title	Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints
Keywords keywords	Double-helix RNA, Protein-RNA complex, Swiss Jelly-roll beta barrel, icosahedral virus, 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.

4nia__assembly_1__model_1

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

Download this curve (.dat)

4nia__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4nia__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	69.64 Å
Rg (electron density)	70.80 Å
Total Rg	70.66 Å
Atom count	80888
Residues	9312
Excluded volume	1386500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4nia__assembly_1__model_1`	240-meric （240）	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 (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	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	28403

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

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	3381

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d4niaa_
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	d4niab_
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	d4niac_
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	d4niad_
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	d4niae_
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	d4niaf_
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	d4niag_
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	d4niah_
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	d4niai_
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	d4niaj_
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	d4niak_
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	d4nial_
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	d4niam_
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	d4nian_
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	d4niao_
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	4niaA00
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	4niaB00
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	4niaC00
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	4niaD00
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	4niaE00
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	4niaF00
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	4niaG00
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	4niaH00
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	4niaI00
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	4niaJ00
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	4niaK00
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	4niaL00
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	4niaM00
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	4niaN00
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	4niaO00
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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Unit-cell length a length_a	174.268 Å
Unit-cell length b length_b	191.774 Å
Unit-cell length c length_c	202.503 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	1.820 Å
Low-resolution limit resolution_low	87.040 Å
R factor r_factor	0.1240
R_work r_work	0.1230
R_free r_free	0.1560

Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS 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

4nia__assembly_1__model_1

4nia__assembly_1__model_1 | I(q)

4nia__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) 30 domains

SCOP 2.08 (15 domains)

CATH v4.4 (15 domains)

7. Citations (6)

Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS 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

4nia__assembly_1__model_1

4nia__assembly_1__model_1 | I(q)

4nia__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) 30 domains

SCOP 2.08 (15 domains)

CATH v4.4 (15 domains)

7. Citations (6)