SAXSdb — 9y2z

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

Capsid protein

OrganismNot specified

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 1–351 Chain B； UniProt 1–351 Chain C； UniProt 1–351	Fragment：R domain	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 5.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.87 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 9Y2Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ZX8 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-MERIC	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE；pH 7.4；10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 11.50 Å
3ZX8 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE；pH 7.4；10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 11.50 Å
3ZX8 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE；pH 7.4；10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 11.50 Å
3ZX8 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE；pH 7.4；10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 11.50 Å
3ZX8 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE；pH 7.4；10 MM SODIUM PHOSPHATE PH 7.4, 10 MM MAGNESIUM SULPHATE cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 11.50 Å
3ZX9 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-MERIC	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 MM TRIS PH 8.5, 5 MM EDTA；pH 8.5；100 MM TRIS PH 8.5, 5 MM EDTA cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 17.00 Å
3ZX9 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 MM TRIS PH 8.5, 5 MM EDTA；pH 8.5；100 MM TRIS PH 8.5, 5 MM EDTA cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 17.00 Å
3ZX9 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 MM TRIS PH 8.5, 5 MM EDTA；pH 8.5；100 MM TRIS PH 8.5, 5 MM EDTA cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 17.00 Å
3ZX9 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 MM TRIS PH 8.5, 5 MM EDTA；pH 8.5；100 MM TRIS PH 8.5, 5 MM EDTA cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 17.00 Å
3ZX9 Cryo-EM reconstruction of native and expanded Turnip Crinkle virus Deposited 2011-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–221（221 aa） Chain A 225–246（22 aa） Chain A 248–351（104 aa） Chain B 1–221（221 aa） Chain B 225–246（22 aa） Chain B 248–351（104 aa） Chain C 1–221（221 aa） Chain C 225–246（22 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 MM TRIS PH 8.5, 5 MM EDTA；pH 8.5；100 MM TRIS PH 8.5, 5 MM EDTA cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- DOUBLE SIDED AUTOMATED BLOTTER AND PLUNGER, METHOD- BLOT 1.6 SECONDS BEFORE PLUNGING,	Resolution 17.00 Å
3ZXA Structure and Assembly of Turnip Crinkle Virus I. X-ray Crystallographic Structure Analysis at 3.2 A Resolution Deposited 2011-08-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-MERIC	Chain C 1–220（220 aa） Chain C 224–246（23 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；THE METHYL MERCURY ADDUCT WAS OBTAINED BY BRINGING STOCK SOLUTION OF VIRUS (3.5% TCV (W/V) IN 0.01% SODIUM AZIDE,) TO 6 EQUIVALENT METHYL MERCURY/PROTEIN SUBUNIT BY ADDITION OF 15 MILLIMOLAR-METHYL MERCURY NITRATE AND INCUBATING FOR 1 H. CRYSTALLIZATION WAS THEN INITIATED BY ADDITION OF AN APPROXIMATELY EQUAL VOLUME OF SATURATED SODIUM CITRATE (PH 7.0) AND ALLOWED TO PROCEED UNDISTURBED FOR 2 TO 4 MONTHS. THE OPTIMUM CONCENTRATION OF SODIUM CITRATE REQUIRED TO PRODUCE LARGE CRYSTALS VARIED FROM EXPERIMENT TO EXPERIMENT BUT WAS GENERALLY IN THE RANGE 42 TO 46% SATURATED.	Resolution 3.20 Å
3ZXA Structure and Assembly of Turnip Crinkle Virus I. X-ray Crystallographic Structure Analysis at 3.2 A Resolution Deposited 2011-08-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–220（220 aa） Chain C 224–246（23 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；THE METHYL MERCURY ADDUCT WAS OBTAINED BY BRINGING STOCK SOLUTION OF VIRUS (3.5% TCV (W/V) IN 0.01% SODIUM AZIDE,) TO 6 EQUIVALENT METHYL MERCURY/PROTEIN SUBUNIT BY ADDITION OF 15 MILLIMOLAR-METHYL MERCURY NITRATE AND INCUBATING FOR 1 H. CRYSTALLIZATION WAS THEN INITIATED BY ADDITION OF AN APPROXIMATELY EQUAL VOLUME OF SATURATED SODIUM CITRATE (PH 7.0) AND ALLOWED TO PROCEED UNDISTURBED FOR 2 TO 4 MONTHS. THE OPTIMUM CONCENTRATION OF SODIUM CITRATE REQUIRED TO PRODUCE LARGE CRYSTALS VARIED FROM EXPERIMENT TO EXPERIMENT BUT WAS GENERALLY IN THE RANGE 42 TO 46% SATURATED.	Resolution 3.20 Å
3ZXA Structure and Assembly of Turnip Crinkle Virus I. X-ray Crystallographic Structure Analysis at 3.2 A Resolution Deposited 2011-08-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain C 1–220（220 aa） Chain C 224–246（23 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；THE METHYL MERCURY ADDUCT WAS OBTAINED BY BRINGING STOCK SOLUTION OF VIRUS (3.5% TCV (W/V) IN 0.01% SODIUM AZIDE,) TO 6 EQUIVALENT METHYL MERCURY/PROTEIN SUBUNIT BY ADDITION OF 15 MILLIMOLAR-METHYL MERCURY NITRATE AND INCUBATING FOR 1 H. CRYSTALLIZATION WAS THEN INITIATED BY ADDITION OF AN APPROXIMATELY EQUAL VOLUME OF SATURATED SODIUM CITRATE (PH 7.0) AND ALLOWED TO PROCEED UNDISTURBED FOR 2 TO 4 MONTHS. THE OPTIMUM CONCENTRATION OF SODIUM CITRATE REQUIRED TO PRODUCE LARGE CRYSTALS VARIED FROM EXPERIMENT TO EXPERIMENT BUT WAS GENERALLY IN THE RANGE 42 TO 46% SATURATED.	Resolution 3.20 Å
3ZXA Structure and Assembly of Turnip Crinkle Virus I. X-ray Crystallographic Structure Analysis at 3.2 A Resolution Deposited 2011-08-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 1–220（220 aa） Chain C 224–246（23 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；THE METHYL MERCURY ADDUCT WAS OBTAINED BY BRINGING STOCK SOLUTION OF VIRUS (3.5% TCV (W/V) IN 0.01% SODIUM AZIDE,) TO 6 EQUIVALENT METHYL MERCURY/PROTEIN SUBUNIT BY ADDITION OF 15 MILLIMOLAR-METHYL MERCURY NITRATE AND INCUBATING FOR 1 H. CRYSTALLIZATION WAS THEN INITIATED BY ADDITION OF AN APPROXIMATELY EQUAL VOLUME OF SATURATED SODIUM CITRATE (PH 7.0) AND ALLOWED TO PROCEED UNDISTURBED FOR 2 TO 4 MONTHS. THE OPTIMUM CONCENTRATION OF SODIUM CITRATE REQUIRED TO PRODUCE LARGE CRYSTALS VARIED FROM EXPERIMENT TO EXPERIMENT BUT WAS GENERALLY IN THE RANGE 42 TO 46% SATURATED.	Resolution 3.20 Å
3ZXA Structure and Assembly of Turnip Crinkle Virus I. X-ray Crystallographic Structure Analysis at 3.2 A Resolution Deposited 2011-08-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–220（220 aa） Chain C 224–246（23 aa） Chain C 248–351（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；THE METHYL MERCURY ADDUCT WAS OBTAINED BY BRINGING STOCK SOLUTION OF VIRUS (3.5% TCV (W/V) IN 0.01% SODIUM AZIDE,) TO 6 EQUIVALENT METHYL MERCURY/PROTEIN SUBUNIT BY ADDITION OF 15 MILLIMOLAR-METHYL MERCURY NITRATE AND INCUBATING FOR 1 H. CRYSTALLIZATION WAS THEN INITIATED BY ADDITION OF AN APPROXIMATELY EQUAL VOLUME OF SATURATED SODIUM CITRATE (PH 7.0) AND ALLOWED TO PROCEED UNDISTURBED FOR 2 TO 4 MONTHS. THE OPTIMUM CONCENTRATION OF SODIUM CITRATE REQUIRED TO PRODUCE LARGE CRYSTALS VARIED FROM EXPERIMENT TO EXPERIMENT BUT WAS GENERALLY IN THE RANGE 42 TO 46% SATURATED.	Resolution 3.20 Å
9GDW RNA binding domain of Turnip crinkle virus p38, p38R Deposited 2024-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–45（45 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；283 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9QVF Turnip Crinkle Virus: virus-like particles (TCV-P38+1) Deposited 2025-04-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric	Chain A 1–351（351 aa） Chain B 1–351（351 aa） Chain C 1–351（351 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；1 mM MgSO4 1mM NaPO4 and pH7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9QVG Turnip Crinkle Virus: virions (TCV-M) Deposited 2025-04-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric	Chain A 1–351（351 aa） Chain B 1–351（351 aa） Chain C 1–351（351 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；1 mM MgSO4 1mM NaPO4 and pH7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
9QVH Turnip Crinkle Virus: virus-like particles (TCV-P38) Deposited 2025-04-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric	Chain A 1–351（351 aa） Chain B 1–351（351 aa） Chain C 1–351（351 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；1 mM MgSO4 1mM NaPO4 and pH7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
9Y31 Symmetry relaxed asymmetric structure of an expansion intermediate of Turnip crinkle virus Deposited 2025-09-01	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 1–351（351 aa） Fragment：R domain Chain E 1–351（351 aa） Fragment：R domain Chain H 1–351（351 aa） Fragment：R domain	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 5.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å

8 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CAPSD_TCV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–351； UniProt 1–351 Author chain B； PDBConstruct 1–351； UniProt 1–351 Author chain C； PDBConstruct 1–351； UniProt 1–351

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	9y2z
Deposition date deposition_date	2025-09-01
Structure title title	Icosahedral symmetric structure of an expansion intermediate of Turnip Crinkle Virus (Asymmetric Trimer Unit)
Keywords keywords	Icosahedral non-enveloped ssRNA virus, Expansion intermediate, VIRUS; VIRUS
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	32.86 Å
Radius of gyration Rg (electron density) rg_electron	31.98 Å
Forward intensity I(0) i0	130194000.00
Molecular weight molecular_weight	88350.0 kDa
Excluded volume excluded_volume	109880 Å³
Envelope volume envelope_volume	160800 Å³
Hydration-shell volume shell_volume	41711 Å³
Envelope diameter envelope_diameter	115.5 Å
Shell Rg shell_rg	39.01 Å
Envelope Rg envelope_rg	31.47 Å
Shape Rg shape_rg	31.95 Å
Total Rg total_rg	32.69 Å
Total atoms total_atoms	6230
Residues n_residues	842
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	109.2 Å
Rg (real space) rg_real	32.64 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	1.3020e+08
I(0) uncertainty (real space) i0_real_error	2.5380e+06
Rg (reciprocal space) rg_reciprocal	32.74 Å
I(0) (reciprocal space) i0_reciprocal	130200000.0000
Solution quality estimate total_estimate	0.8777
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.2 Å
Skewness Skewness skewness	0.117
Kurtosis Kurtosis kurtosis	-0.372
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14620000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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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	—

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

Resolution resolution	2.870 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.87 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	60938

Description description	Capsid protein
Molecular weight formula_weight	38170.9 kDa
Source method src_method	nat
Copy count entity_count	3

Icosahedral symmetric structure of an expansion intermediate of Turnip Crinkle Virus (Asymmetric Trimer Unit)

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

Capsid 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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6230

fit	/app/data/saxs_computation/y2/9y2z/9y2z.fit
pddf	/app/data/pr_computation/y2/9y2z/9y2z.pr.out
profile	/app/data/saxs_computation/y2/9y2z/9y2z.dat