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3zx9

Cryo-EM reconstruction of native and expanded Turnip Crinkle virus

Method: ELECTRON MICROSCOPY Dmax: 110.0 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 × 180 PDB declaration: 180-MERIC（180） Consistent with protein copy count Chain A； UniProt 1–221 Chain A； UniProt 225–246 Chain A； UniProt 248–351 Chain B； UniProt 1–221 Chain B； UniProt 225–246 Chain B； UniProt 248–351 Chain C； UniProt 1–221 Chain C； UniProt 225–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–221 Chain A； UniProt 225–246 Chain A； UniProt 248–351 Chain B； UniProt 1–221 Chain B； UniProt 225–246 Chain B； UniProt 248–351 Chain C； UniProt 1–221 Chain C； UniProt 225–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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
3 Protein homooligomer Homooligomer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain A； UniProt 1–221 Chain A； UniProt 225–246 Chain A； UniProt 248–351 Chain B； UniProt 1–221 Chain B； UniProt 225–246 Chain B； UniProt 248–351 Chain C； UniProt 1–221 Chain C； UniProt 225–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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
4 Protein homooligomer Homooligomer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain A； UniProt 1–221 Chain A； UniProt 225–246 Chain A； UniProt 248–351 Chain B； UniProt 1–221 Chain B； UniProt 225–246 Chain B； UniProt 248–351 Chain C； UniProt 1–221 Chain C； UniProt 225–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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
5 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–221 Chain A； UniProt 225–246 Chain A； UniProt 248–351 Chain B； UniProt 1–221 Chain B； UniProt 225–246 Chain B； UniProt 248–351 Chain C； UniProt 1–221 Chain C； UniProt 225–246 Chain C； UniProt 248–351 Not recorded No other associated polymer 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

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 3ZX9 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 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 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 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 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 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
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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 A； PDBConstruct 1–221； UniProt 1–221 Author chain A； PDBConstruct 222–243； UniProt 225–246 Author chain A； PDBConstruct 244–347； UniProt 248–351 Author chain B； PDBConstruct 1–221； UniProt 1–221 Author chain B； PDBConstruct 222–243； UniProt 225–246 Author chain B； PDBConstruct 244–347； UniProt 248–351 Author chain C； PDBConstruct 1–221； UniProt 1–221 Author chain C； PDBConstruct 222–243； UniProt 225–246 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 3zx9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3zx9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3zx9
Deposition date deposition_date2011-08-08
Structure title titleCryo-EM reconstruction of native and expanded Turnip Crinkle virus
Keywords keywordsVIRUS, GENOMIC RNA STRUCTURE, GENOME UNCOATING, SSRNA VIRUS, ICOSAHEDRAL; VIRUS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.19 Å
Radius of gyration Rg (electron density) rg_electron34.47 Å
Forward intensity I(0) i0125177000.00
Molecular weight molecular_weight89069.0 kDa
Excluded volume excluded_volume111460 ų
Envelope volume envelope_volume160820 ų
Hydration-shell volume shell_volume39196 ų
Envelope diameter envelope_diameter116.2 Å
Shell Rg shell_rg41.14 Å
Envelope Rg envelope_rg33.14 Å
Shape Rg shape_rg34.45 Å
Total Rg total_rg35.10 Å
Total atoms total_atoms6284
Residues n_residues829
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 dmax110.0 Å
Rg (real space) rg_real35.00 Å
Rg uncertainty (real space) rg_real_error0.80 Å
I(0) (real space) i0_real1.2520e+08
I(0) uncertainty (real space) i0_real_error1.8990e+06
Rg (reciprocal space) rg_reciprocal35.12 Å
I(0) (reciprocal space) i0_reciprocal125200000.0000
Solution quality estimate total_estimate0.8883
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.9 Å
Skewness Skewness skewness0.045
Kurtosis Kurtosis kurtosis-0.448
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7860000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.965
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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 (2)

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9. Files and Curves (10)