SAXSdb — 1za7

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

Coat protein

Cowpea chlorotic 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 homooligomer Homooligomer Protein × 180 PDB declaration: 180-MERIC（180） Consistent with protein copy count	Chain A； UniProt 25–189 Chain B； UniProt 25–189 Chain C； UniProt 25–189	Mutation：K42R	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.3；298 K；0.3M succinate, 4% PEG 8000, pH 3.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 3.30	Resolution 2.70 Å
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 25–189 Chain B； UniProt 25–189 Chain C； UniProt 25–189	Mutation：K42R	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.3；298 K；0.3M succinate, 4% PEG 8000, pH 3.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 3.30	Resolution 2.70 Å
3	Protein homooligomer Homooligomer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain A； UniProt 25–189 Chain B； UniProt 25–189 Chain C； UniProt 25–189	Mutation：K42R	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.3；298 K；0.3M succinate, 4% PEG 8000, pH 3.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 3.30	Resolution 2.70 Å
4	Protein homooligomer Homooligomer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count	Chain A； UniProt 25–189 Chain B； UniProt 25–189 Chain C； UniProt 25–189	Mutation：K42R	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.3；298 K；0.3M succinate, 4% PEG 8000, pH 3.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 3.30	Resolution 2.70 Å
5	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 25–189 Chain B； UniProt 25–189 Chain C； UniProt 25–189	Mutation：K42R	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.3；298 K；0.3M succinate, 4% PEG 8000, pH 3.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 3.30	Resolution 2.70 Å
6	Protein homooligomer Homooligomer Protein × 180 PDB declaration: 180-meric（180） Consistent with protein copy count	Chain A； UniProt 25–189 Chain B； UniProt 25–189 Chain C； UniProt 25–189	Mutation：K42R	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.3；298 K；0.3M succinate, 4% PEG 8000, pH 3.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 3.30	Resolution 2.70 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 1ZA7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CWP STRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MOTTLE VIRUS DETERMINED BY X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY Deposited 1995-05-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 180 PDB declaration: 360-MERIC	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å
1CWP STRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MOTTLE VIRUS DETERMINED BY X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY Deposited 1995-05-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Homooligomer；Protein × 3 PDB declaration: hexameric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å
1CWP STRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MOTTLE VIRUS DETERMINED BY X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY Deposited 1995-05-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Homooligomer；Protein × 15 PDB declaration: 30-meric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å
1CWP STRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MOTTLE VIRUS DETERMINED BY X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY Deposited 1995-05-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Homooligomer；Protein × 18 PDB declaration: 36-meric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å
1CWP STRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MOTTLE VIRUS DETERMINED BY X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY Deposited 1995-05-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–RNA Homooligomer；Protein × 3 PDB declaration: hexameric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å
1CWP STRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MOTTLE VIRUS DETERMINED BY X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY Deposited 1995-05-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein–RNA Homooligomer；Protein × 180 PDB declaration: 360-meric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å
8C38 Contracted cowpea chlorotic mottle virus Deposited 2022-12-23	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric	Chain C 1–190（190 aa） Chain D 1–190（190 aa） Chain I 1–190（190 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.64 Å
8CPY Extended cowpea chlorotic mottle virus Deposited 2023-03-03	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric	Chain C 1–190（190 aa） Chain D 1–190（190 aa） Chain I 1–190（190 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 4.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

3 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COAT_CCMV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–165； UniProt 25–189 Author chain B； PDBConstruct 1–165； UniProt 25–189 Author chain C； PDBConstruct 1–165； UniProt 25–189

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	1za7
Deposition date deposition_date	2005-04-05
Structure title title	The crystal structure of salt stable cowpea cholorotic mottle virus at 2.7 angstroms resolution.
Keywords keywords	;mutant virus capsid structure, icosahedral particle, stablizing mutation, stable mutant, beta hexamer, beta barrel, bromovirus, point mutation, Icosahedral virus, Virus ;; VIRUS
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	28.80 Å
Radius of gyration Rg (electron density) rg_electron	28.19 Å
Forward intensity I(0) i0	41249700.00
Molecular weight molecular_weight	51304.0 kDa
Excluded volume excluded_volume	64950 Å³
Envelope volume envelope_volume	93056 Å³
Hydration-shell volume shell_volume	27559 Å³
Envelope diameter envelope_diameter	102.0 Å
Shell Rg shell_rg	34.79 Å
Envelope Rg envelope_rg	29.61 Å
Shape Rg shape_rg	28.15 Å
Total Rg total_rg	29.07 Å
Total atoms total_atoms	3615
Residues n_residues	481
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	95.7 Å
Rg (real space) rg_real	28.81 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	4.1250e+07
I(0) uncertainty (real space) i0_real_error	6.0430e+05
Rg (reciprocal space) rg_reciprocal	28.81 Å
I(0) (reciprocal space) i0_reciprocal	41250000.0000
Solution quality estimate total_estimate	0.8931
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.3 Å
Skewness Skewness skewness	0.302
Kurtosis Kurtosis kurtosis	-0.412
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7090000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1za7a_
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.121.4.5 — Bromoviridae-like VP

Domain ID domain_id	d1za7b_
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.121.4.5 — Bromoviridae-like VP

Domain ID domain_id	d1za7c_
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.121.4.5 — Bromoviridae-like VP

CATH v4.4 (3 domains)

Domain ID domain_id	1za7A00
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	1za7B01
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	1za7C01
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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8. Citations (4)

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Unit-cell length a length_a	365.480 Å
Unit-cell length b length_b	374.860 Å
Unit-cell length c length_c	402.490 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	720

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2450
R_work r_work	0.2450
R_free r_free	—

Description description	Coat protein
Molecular weight formula_weight	17601.0 kDa
Mutation mutation	K42R
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3741

The crystal structure of salt stable cowpea cholorotic mottle virus at 2.7 angstroms resolution.

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

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Cowpea chlorotic mottle virus
NCBI Class编号 ncbi_taxonomy_id	12303
宿主生物 host_organism	Vigna unguiculata

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

fit	/app/data/saxs_computation/za/1za7/1za7.fit
pddf	/app/data/pr_computation/za/1za7/1za7.pr.out
profile	/app/data/saxs_computation/za/1za7/1za7.dat