1kvp

STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY

Method: ELECTRON MICROSCOPY

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

SPV4 CAPSID PROTEIN VP1

Enterobacteria phage phiX174

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	No other associated polymer	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	No other associated polymer	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGF_BPPHX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–497； UniProt 1–426

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	1kvp
Deposition date deposition_date	1997-12-12
Structure title title	STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY
Keywords keywords	BACTERIOPHAGE SPV4 COAT PROTEIN, CHIMERA, Icosahedral virus, Virus; VIRUS
Experimental Method method	ELECTRON MICROSCOPY

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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.

1kvp__assembly_1__model_1

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

Download this curve (.dat)

1kvp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kvp__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)	124.50 Å
Total Rg	124.50 Å
Atom count	0
Residues	0
Excluded volume	4081600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kvp__assembly_1__model_1`	60-MERIC （60）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1kvp__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1kvp__assembly_3__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1kvp__assembly_4__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1kvp__assembly_5__model_1`	monomeric （1）	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 (1)

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6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1kvpa_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.1 — Microviridae-like VP

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	27.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	27.00 Å
Resolution测定Method resolution_method	;COMMON-LINES AND POLAR-FOURIER-TRANSFORM FULLER ET AL. 1996, J.STRUC.BIOL.c 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130 ;
颗粒数 num_particles	—

Description description	SPV4 CAPSID PROTEIN VP1
Molecular weight formula_weight	55834.7 kDa
Source method src_method	man
Copy count entity_count	1

STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY

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

SPV4 CAPSID PROTEIN VP1

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

1kvp__assembly_1__model_1

1kvp__assembly_1__model_1 | I(q)

1kvp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	497

Source organism organism	Enterobacteria phage phiX174
NCBI taxonomy ID ncbi_taxonomy_id	10847
Host organism host_organism	Spiroplasma melliferum

STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY

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

SPV4 CAPSID PROTEIN VP1

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

1kvp__assembly_1__model_1

1kvp__assembly_1__model_1 | I(q)

1kvp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (3)