SAXSdb — 6msf

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

PROTEIN (MS2 PROTEIN CAPSID)

Enterobacterio phage MS2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 180 RNA 120	;RNA (5'-R(CPCPAPCPAPGPUPCPAPCPUPGPGPG)-3') ; × 60 ;RNA (5'-R(CPAPGPUPCPAPCPUPGPG)-3') ; × 60 water × 300	Consistent with all polymers
2	Protein–RNA	Homooligomer	Protein 3 RNA 2	;RNA (5'-R(CPCPAPCPAPGPUPCPAPCPUPGPGPG)-3') ; × 1 ;RNA (5'-R(CPAPGPUPCPAPCPUPGPG)-3') ; × 1 water × 5	Consistent with all polymers
3	Protein–RNA	Homooligomer	Protein 15 RNA 10	;RNA (5'-R(CPCPAPCPAPGPUPCPAPCPUPGPGPG)-3') ; × 5 ;RNA (5'-R(CPAPGPUPCPAPCPUPGPG)-3') ; × 5 water × 25	Consistent with all polymers
4	Protein–RNA	Homooligomer	Protein 18 RNA 12	;RNA (5'-R(CPCPAPCPAPGPUPCPAPCPUPGPGPG)-3') ; × 6 ;RNA (5'-R(CPAPGPUPCPAPCPUPGPG)-3') ; × 6 water × 30	Consistent with all polymers
5	Protein–RNA	Homooligomer	Protein 3 RNA 2	;RNA (5'-R(CPCPAPCPAPGPUPCPAPCPUPGPGPG)-3') ; × 1 ;RNA (5'-R(CPAPGPUPCPAPCPUPGPG)-3') ; × 1 water × 5	Consistent with all polymers
6	Protein–RNA	Homooligomer	Protein 30 RNA 20	;RNA (5'-R(CPCPAPCPAPGPUPCPAPCPUPGPGPG)-3') ; × 10 ;RNA (5'-R(CPAPGPUPCPAPCPUPGPG)-3') ; × 10 water × 50	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COAT_BPMS2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–129； UniProt 1–129 Author chain B； PDBConstruct 1–129； UniProt 1–129 Author chain C； PDBConstruct 1–129； UniProt 1–129

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	6msf
Deposition date deposition_date	1998-01-06
Structure title title	F6 APTAMER MS2 COAT PROTEIN COMPLEX
Keywords keywords	VIRAL COAT PROTEIN-RNA COMPLEX, RNA APTAMER, RNA STEM LOOP, BACTERIOPHAGE MS2, 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.

6msf__assembly_1__model_1

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

Download this curve (.dat)

6msf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6msf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	119.30 Å
Total Rg	119.10 Å
Atom count	204000
Residues	24660
Excluded volume	3521000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6msf__assembly_1__model_1`	complete icosahedral assembly （300）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6msf__assembly_2__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`6msf__assembly_3__model_1`	25-meric （25）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`6msf__assembly_4__model_1`	30-meric （30）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`6msf__assembly_5__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`6msf__assembly_6__model_1`	50-meric （50）	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 (4)

Entity 1 Entity 1 polymer

Description description	;RNA (5'-R(CPCPAPCPAPGPUPCPAPCPUPGPGPG)-3') ;
Molecular weight formula_weight	4461.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R
Atom count atom_count	3495

CCACAGUCACUGGG

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(CPAPGPUPCPAPCPUPGPG)-3') ;
Molecular weight formula_weight	3176.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	S

CAGUCACUGG

Entity 3 Entity 3 polymer

Description description	PROTEIN (MS2 PROTEIN CAPSID)
Molecular weight formula_weight	13738.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY

Source Source

Source organism organism	Enterobacterio phage MS2
NCBI taxonomy ID ncbi_taxonomy_id	12022
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6msfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.85 — RNA bacteriophage capsid protein
Superfamily Superfamily superfamily	d.85.1 — RNA bacteriophage capsid protein
Family Family family	d.85.1.1 — RNA bacteriophage capsid protein

Domain ID domain_id	d6msfb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.85 — RNA bacteriophage capsid protein
Superfamily Superfamily superfamily	d.85.1 — RNA bacteriophage capsid protein
Family Family family	d.85.1.1 — RNA bacteriophage capsid protein

Domain ID domain_id	d6msfc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.85 — RNA bacteriophage capsid protein
Superfamily Superfamily superfamily	d.85.1 — RNA bacteriophage capsid protein
Family Family family	d.85.1.1 — RNA bacteriophage capsid protein

CATH v4.4 (3 domains)

Domain ID domain_id	6msfA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	380 — MS2 Viral Coat Protein
Homologous superfamily homologous superfamily	10 — MS2 Viral Coat Protein

Domain ID domain_id	6msfB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	380 — MS2 Viral Coat Protein
Homologous superfamily homologous superfamily	10 — MS2 Viral Coat Protein

Domain ID domain_id	6msfC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	380 — MS2 Viral Coat Protein
Homologous superfamily homologous superfamily	10 — MS2 Viral Coat Protein

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Unit-cell length a length_a	287.580 Å
Unit-cell length b length_b	287.580 Å
Unit-cell length c length_c	652.190 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	540

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	36.000 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2010

F6 APTAMER MS2 COAT PROTEIN COMPLEX

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

PROTEIN (MS2 PROTEIN CAPSID)

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

6msf__assembly_1__model_1

6msf__assembly_1__model_1 | I(q)

6msf__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (4)

F6 APTAMER MS2 COAT PROTEIN COMPLEX

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

PROTEIN (MS2 PROTEIN CAPSID)

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

6msf__assembly_1__model_1

6msf__assembly_1__model_1 | I(q)

6msf__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (4)