6wbs

Human CFTR first nucleotide binding domain with dF508/V510D

Method: X-RAY DIFFRACTION Dmax: 76.2 Å Quality: EXCELLENT

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

Cystic fibrosis transmembrane conductance regulator

Homo sapiens

UniProt P13569

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 388–646 Mutation:deltaF508, V510D, delta405-436 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;CFTR NBD1 V510D in buffer A was crystallized by mixing equal amounts of protein at 6 mg/mL with 0.1 M Tris pH 7.6, 28% (w/v) polyethylene glycol 10,000. Crystallization was induced by streak-seeding using crystals grown in 0.1 M HEPES, pH 7.5, 25% (w/v) polyethylene glycol 550 monomethylether, and plates incubated at 4C. Crystals grew over several days and were frozen by quick dip in reservoir solution supplemented with 25% (w/v) ethylene glycol Resolution 1.86 Å R-free 0.213
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 388–646 Mutation:deltaF508, V510D, delta405-436 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;CFTR NBD1 V510D in buffer A was crystallized by mixing equal amounts of protein at 6 mg/mL with 0.1 M Tris pH 7.6, 28% (w/v) polyethylene glycol 10,000. Crystallization was induced by streak-seeding using crystals grown in 0.1 M HEPES, pH 7.5, 25% (w/v) polyethylene glycol 550 monomethylether, and plates incubated at 4C. Crystals grew over several days and were frozen by quick dip in reservoir solution supplemented with 25% (w/v) ethylene glycol Resolution 1.86 Å R-free 0.213

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.

52 other PDB entries and 69 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CFTR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–226; UniProt 388–646 Author chain B; PDBConstruct 1–226; UniProt 388–646

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 6wbs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6wbs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6wbs
Deposition date deposition_date2020-03-27
Structure title titleHuman CFTR first nucleotide binding domain with dF508/V510D
Keywords keywordsIon Channel, ATP Binding, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.21
Radius of gyration Rg (electron density) rg_electron24.32
Forward intensity I(0) i042429800.00
Molecular weight molecular_weight49996.0 kDa
Excluded volume excluded_volume62543 ų
Envelope volume envelope_volume77231 ų
Hydration-shell volume shell_volume26485 ų
Envelope diameter envelope_diameter77.2
Shell Rg shell_rg31.33
Envelope Rg envelope_rg24.25
Shape Rg shape_rg24.33
Total Rg total_rg25.13
Total atoms total_atoms6978
Residues n_residues440
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 dmax76.2
Rg (real space) rg_real25.12
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real4.2430e+07
I(0) uncertainty (real space) i0_real_error6.1480e+05
Rg (reciprocal space) rg_reciprocal25.15
I(0) (reciprocal space) i0_reciprocal42430000.0000
Solution quality estimate total_estimate0.9156
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.0
Skewness Skewness skewness0.165
Kurtosis Kurtosis kurtosis-0.616
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8634000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6wbsa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like
Domain ID domain_idd6wbsb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like

8. Citations (1)

9. Files and Curves (10)