5tfn

CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE in super-open conformation

Method: X-RAY DIFFRACTION Dmax: 71.7 Å Quality: GOOD

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

NS2B-NS3 Protease CHIMERA,Genome polyprotein

Zika virus

UniProt A0A160JCU6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1420–1466 Mutation:S135A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5) Resolution 3.00 Å R-free 0.259
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1420–1466 Mutation:S135A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5) Resolution 3.00 Å R-free 0.259
3 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1420–1466 Chain B; UniProt 1420–1466 Mutation:S135A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5) Resolution 3.00 Å R-free 0.259

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.

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

View Construct and Data Evidence
UniProt name A0A160JCU6_ZIKV
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–49; UniProt 1420–1466 Author chain B; PDBConstruct 3–49; UniProt 1420–1466

NS2B-NS3 Protease CHIMERA,Genome polyprotein

Zika virus

UniProt Q32ZE1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1499–1680 Mutation:S135A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5) Resolution 3.00 Å R-free 0.259
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1499–1680 Mutation:S135A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5) Resolution 3.00 Å R-free 0.259
3 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1499–1680 Chain B; UniProt 1499–1680 Mutation:S135A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5) Resolution 3.00 Å R-free 0.259

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.

263 other PDB entries and 300 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_ZIKV
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 60–241; UniProt 1499–1680 Author chain B; PDBConstruct 60–241; UniProt 1499–1680

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 5tfn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tfn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tfn
Deposition date deposition_date2016-09-26
Structure title titleCRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE in super-open conformation
Keywords keywordsFlavivirus, SERINE PROTEASE, Zika virus, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.91
Radius of gyration Rg (electron density) rg_electron20.99
Forward intensity I(0) i021941700.00
Molecular weight molecular_weight35076.0 kDa
Excluded volume excluded_volume43689 ų
Envelope volume envelope_volume53506 ų
Hydration-shell volume shell_volume21517 ų
Envelope diameter envelope_diameter72.1
Shell Rg shell_rg27.22
Envelope Rg envelope_rg21.17
Shape Rg shape_rg20.99
Total Rg total_rg21.83
Total atoms total_atoms2469
Residues n_residues325
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax71.7
Rg (real space) rg_real21.88
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real2.1940e+07
I(0) uncertainty (real space) i0_real_error2.5510e+05
Rg (reciprocal space) rg_reciprocal21.88
I(0) (reciprocal space) i0_reciprocal21940000.0000
Solution quality estimate total_estimate0.8905
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6
Skewness Skewness skewness0.323
Kurtosis Kurtosis kurtosis-0.392
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8303000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id5tfnB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily120

8. Citations (1)

9. Files and Curves (10)