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3zxa

Structure and Assembly of Turnip Crinkle Virus I. X-ray Crystallographic Structure Analysis at 3.2 A Resolution

Method: X-RAY DIFFRACTION Dmax: 76.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CAPSID PROTEIN

OrganismNot specified

UniProt P06663

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 × 60 PDB declaration: 60-MERIC（60） Consistent with protein copy count Chain C； UniProt 1–220 Chain C； UniProt 224–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–220 Chain C； UniProt 224–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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
3 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain C； UniProt 1–220 Chain C； UniProt 224–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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
4 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain C； UniProt 1–220 Chain C； UniProt 224–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–220 Chain C； UniProt 224–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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

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 3ZXA 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 oligomeric state Different experimental method 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 method 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 method 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 method 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 method 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 oligomeric state Different experimental method 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 method 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 method 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 method 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 method 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
9GDW RNA binding domain of Turnip crinkle virus p38, p38R Deposited 2024-08-06 Different construct Different mutation/modification 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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
9Y2Z Icosahedral symmetric structure of an expansion intermediate of Turnip Crinkle Virus (Asymmetric Trimer Unit) Deposited 2025-09-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric
Chain A 1–351（351 aa） Fragment：R domain
Chain B 1–351（351 aa） Fragment：R domain
Chain C 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 2.87 Å
9Y31 Symmetry relaxed asymmetric structure of an expansion intermediate of Turnip crinkle virus Deposited 2025-09-01 Different construct Different oligomeric state Different experimental method Different experimental conditions 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 16 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 C； PDBConstruct 1–220； UniProt 1–220 Author chain C； PDBConstruct 221–243； UniProt 224–246 Author chain C； PDBConstruct 244–347； UniProt 248–351

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3zxa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3zxa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3zxa
Deposition date deposition_date2011-08-08
Structure title titleStructure and Assembly of Turnip Crinkle Virus I. X-ray Crystallographic Structure Analysis at 3.2 A Resolution
Keywords keywordsVIRUS, SSRNA VIRUS, ICOSAHEDRAL VIRUS; VIRUS
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.91 Å
Radius of gyration Rg (electron density) rg_electron21.00 Å
Forward intensity I(0) i017827900.00
Molecular weight molecular_weight31714.0 kDa
Excluded volume excluded_volume39672 ų
Envelope volume envelope_volume50085 ų
Hydration-shell volume shell_volume20347 ų
Envelope diameter envelope_diameter79.3 Å
Shell Rg shell_rg27.02 Å
Envelope Rg envelope_rg21.47 Å
Shape Rg shape_rg20.97 Å
Total Rg total_rg21.92 Å
Total atoms total_atoms2237
Residues n_residues295
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax76.8 Å
Rg (real space) rg_real21.88 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real1.7830e+07
I(0) uncertainty (real space) i0_real_error2.2540e+05
Rg (reciprocal space) rg_reciprocal21.88 Å
I(0) (reciprocal space) i0_reciprocal17830000.0000
Solution quality estimate total_estimate0.7889
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary68.7 Å
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.190
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3954000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.774; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.000
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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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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3zxaC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3zxaC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily3420 —
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8. Citations (1)

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9. Files and Curves (10)