SAXSdb — 1bmv

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

PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)

Bean pod mottle virus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Homooligomer Protein × 120 RNA 60 PDB declaration: complete icosahedral assembly（180） Consistent with all polymer counts	Chain 1； UniProt 821–1018 Chain 2； UniProt 447–820	Not recorded	;RNA (5'-R(GPGPUPCPAPAPAPAPUPGP*C)-3') ; × 60	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.00 Å
2	Protein–RNA Homooligomer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain 1； UniProt 821–1018 Chain 2； UniProt 447–820	Not recorded	;RNA (5'-R(GPGPUPCPAPAPAPAPUPGP*C)-3') ; × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.00 Å
3	Protein–RNA Homooligomer Protein × 10 RNA 5 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain 1； UniProt 821–1018 Chain 2； UniProt 447–820	Not recorded	;RNA (5'-R(GPGPUPCPAPAPAPAPUPGP*C)-3') ; × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.00 Å
4	Protein–RNA Homooligomer Protein × 12 RNA 6 PDB declaration: octadecameric（18） Consistent with all polymer counts	Chain 1； UniProt 821–1018 Chain 2； UniProt 447–820	Not recorded	;RNA (5'-R(GPGPUPCPAPAPAPAPUPGP*C)-3') ; × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.00 Å
5	Protein–RNA Homooligomer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain 1； UniProt 821–1018 Chain 2； UniProt 447–820	Not recorded	;RNA (5'-R(GPGPUPCPAPAPAPAPUPGP*C)-3') ; × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.00 Å
6	Protein–RNA Homooligomer Protein × 60 RNA 30 PDB declaration: 90-meric（90） Consistent with all polymer counts	Chain 1； UniProt 821–1018 Chain 2； UniProt 447–820	Not recorded	;RNA (5'-R(GPGPUPCPAPAPAPAPUPGP*C)-3') ; × 30	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1BMV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PGL BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT Deposited 2003-05-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 120 PDB declaration: 180-MERIC	Chain 1 821–1005（185 aa） Chain 2 447–816（370 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.80 Å
1PGL BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT Deposited 2003-05-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain 1 821–1005（185 aa） Chain 2 447–816（370 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.80 Å
1PGL BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT Deposited 2003-05-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Homooligomer；Protein × 10 PDB declaration: pentadecameric	Chain 1 821–1005（185 aa） Chain 2 447–816（370 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.80 Å
1PGL BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT Deposited 2003-05-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Homooligomer；Protein × 12 PDB declaration: octadecameric	Chain 1 821–1005（185 aa） Chain 2 447–816（370 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.80 Å
1PGL BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT Deposited 2003-05-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain 1 821–1005（185 aa） Chain 2 447–816（370 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.80 Å
1PGL BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT Deposited 2003-05-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 90-meric	Chain 1 821–1005（185 aa） Chain 2 447–816（370 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.80 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 120 PDB declaration: 120-MERIC	Chain 1 821–1005（185 aa） Chain 2 466–816（351 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 821–1005（185 aa） Chain 2 466–816（351 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain 1 821–1005（185 aa） Chain 2 466–816（351 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain 1 821–1005（185 aa） Chain 2 466–816（351 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 821–1005（185 aa） Chain 2 466–816（351 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain 1 821–1005（185 aa） Chain 2 466–816（351 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00	Resolution 2.90 Å

2 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGNM_BPMV
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain 1； PDBConstruct 1–185； UniProt 821–1018 Author chain 2； PDBConstruct 1–374； UniProt 447–820

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	1bmv
Deposition date deposition_date	1989-10-09
Structure title title	PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION
Keywords keywords	PROTEIN-RNA COMPLEX, SINGLE STRAND, Icosahedral virus, Virus-RNA COMPLEX; Virus/RNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.24 Å
Radius of gyration Rg (electron density) rg_electron	27.36 Å
Forward intensity I(0) i0	74024500.00
Molecular weight molecular_weight	65379.0 kDa
Excluded volume excluded_volume	80896 Å³
Envelope volume envelope_volume	104410 Å³
Hydration-shell volume shell_volume	32214 Å³
Envelope diameter envelope_diameter	111.7 Å
Shell Rg shell_rg	34.17 Å
Envelope Rg envelope_rg	28.54 Å
Shape Rg shape_rg	27.36 Å
Total Rg total_rg	28.02 Å
Total atoms total_atoms	4570
Residues n_residues	570
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.2 Å
Rg (real space) rg_real	28.34 Å
Rg uncertainty (real space) rg_real_error	1.24 Å
I(0) (real space) i0_real	7.4020e+07
I(0) uncertainty (real space) i0_real_error	1.2500e+06
Rg (reciprocal space) rg_reciprocal	28.31 Å
I(0) (reciprocal space) i0_reciprocal	74020000.0000
Solution quality estimate total_estimate	0.8120
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.6 Å
Skewness Skewness skewness	0.492
Kurtosis Kurtosis kurtosis	-0.027
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13790000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.588; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.790; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;RNA (5'-R(GPGPUPCPAPAPAPAPUPGP*C)-3') ;
Molecular weight formula_weight	3530.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	M
Atom count atom_count	4613

GGUCAAAAUGC

Entity 2 Entity 2 polymer

Description description	PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)
Molecular weight formula_weight	21914.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1

SISQQTVWNQMATVRTPLNFDSSKQSFCQFSVDLLGGGISVDKTGDWITLVQNSPISNLLRVAAWKKGCLMVKVVMSGNAAVKRSDWASLVQVFLTNSNSTEHFDACRWTKSEPHSWELIFPIEVCGPNNGFEMWSSEWANQTSWHLSFLVDNPKQSTTFDVLLGISQNFEIAGNTLMPAFSVPQANARSSENAESSA

来源 Source

来源生物 organism	Bean pod mottle virus
NCBI Class编号 ncbi_taxonomy_id	12260
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)
Molecular weight formula_weight	41223.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

METNLFKLSLDDVETPKGSMLDLKISQSKIALPKNTVGGTILRSDLLANFLTEGNFRASVDLQRTHRIKGMIKMVATVGIPENTGIALACAMNSSIRGRASSDIYTICSQDCELWNPACTKAMTMSFNPNPCSDAWSLEFLKRTGFHCDIICVTGWTATPMQDVQVTIDWFISSQECVPRTYCVLNPQNPFVLNRWMGKLTFPQGTSRSVKRMPLSIGGGAGAKSAILMNMPNAVLSMWRYFVGDLVFEVSKMTSPYIKCTVSFFIAFGNLADDTINFEAFPHKLVQFGEIQEKVVLKFSQEEFLTAWSTQVRPATTLLADGCPYLYAMVHDSSVSTIPGDFVIGVKLTIIENMCAYGLNPGISGSRLLGTIPQ

来源 Source

来源生物 organism	Bean pod mottle virus
NCBI Class编号 ncbi_taxonomy_id	12260
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1bmv11
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.2 — Comoviridae-like VP

Domain ID domain_id	d1bmv21
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.2 — Comoviridae-like VP

Domain ID domain_id	d1bmv22
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.2 — Comoviridae-like VP

CATH v4.4 (2 domains)

Domain ID domain_id	1bmv100
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1bmv200
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	311.200 Å
Unit-cell length b length_b	284.200 Å
Unit-cell length c length_c	350.500 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	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.3300
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/bm/1bmv/1bmv.fit
pddf	/app/data/pr_computation/bm/1bmv/1bmv.pr.out
profile	/app/data/saxs_computation/bm/1bmv/1bmv.dat

PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION

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

PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)