← Back to search
6vwx

NaChBac in lipid nanodisc

Method: ELECTRON MICROSCOPY Dmax: 110.6 Å Quality: GOOD
▼

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

BH1501 protein

Bacillus halodurans C-125

UniProt Q9KCR8

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–274 Chain D； UniProt 1–274 Chain E； UniProt 1–274 Chain F； UniProt 1–274 Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NA SODIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE；blot for 5 seconds before plunging Resolution 3.10 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 6VWX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VX3 NaChBac in GDN Deposited 2020-02-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–274（274 aa）
Chain B 1–274（274 aa）
Chain C 1–274（274 aa）
Chain D 1–274（274 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 10
cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging
Resolution 3.70 Å
6VXO NaChBac-Nav1.7VSDII chimera in nanodisc Deposited 2020-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–97（97 aa）
Chain A 111–274（164 aa）
Chain C 1–97（97 aa）
Chain C 111–274（164 aa）
Chain D 1–97（97 aa）
Chain D 111–274（164 aa）
Chain E 1–97（97 aa）
Chain E 111–274（164 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging
Resolution 3.50 Å
6W6O NaChBac-Nav1.7VSDII chimera and HWTX-IV complex Deposited 2020-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–97（97 aa）
Chain A 111–274（164 aa）
Chain D 1–97（97 aa）
Chain D 111–274（164 aa）
Chain F 1–97（97 aa）
Chain F 111–274（164 aa）
Chain H 1–97（97 aa）
Chain H 111–274（164 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 10
cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 5 seconds before plunging
Resolution 3.20 Å

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

View Construct and Data Evidence
UniProt name Q9KCR8_BACHD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–274； UniProt 1–274 Author chain D； PDBConstruct 1–274； UniProt 1–274 Author chain E； PDBConstruct 1–274； UniProt 1–274 Author chain F； PDBConstruct 1–274； UniProt 1–274

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 6vwx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6vwx
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6vwx
Deposition date deposition_date2020-02-20
Structure title titleNaChBac in lipid nanodisc
Keywords keywordsNaChBac, Channels; Sodium Ion-Selective, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier34.79 Å
Radius of gyration Rg (electron density) rg_electron33.31 Å
Forward intensity I(0) i0128593000.00
Molecular weight molecular_weight109780.0 kDa
Excluded volume excluded_volume145560 ų
Envelope volume envelope_volume188890 ų
Hydration-shell volume shell_volume47218 ų
Envelope diameter envelope_diameter115.2 Å
Shell Rg shell_rg39.99 Å
Envelope Rg envelope_rg33.48 Å
Shape Rg shape_rg33.29 Å
Total Rg total_rg34.00 Å
Total atoms total_atoms7782
Residues n_residues900
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
▼

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

Maximum dimension Dmax dmax110.6 Å
Rg (real space) rg_real34.65 Å
Rg uncertainty (real space) rg_real_error0.96 Å
I(0) (real space) i0_real1.2860e+08
I(0) uncertainty (real space) i0_real_error2.1510e+06
Rg (reciprocal space) rg_reciprocal34.74 Å
I(0) (reciprocal space) i0_reciprocal128600000.0000
Solution quality estimate total_estimate0.8887
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.7 Å
Skewness Skewness skewness0.173
Kurtosis Kurtosis kurtosis-0.348
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10410000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.936
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6vwxa_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.14 — Gated ion channels
Superfamily Superfamily superfamilyf.14.1 — Voltage-gated ion channels
Family Family familyf.14.1.0 — automated matches
Domain ID domain_idd6vwxd_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.14 — Gated ion channels
Superfamily Superfamily superfamilyf.14.1 — Voltage-gated ion channels
Family Family familyf.14.1.0 — automated matches
Domain ID domain_idd6vwxe_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.14 — Gated ion channels
Superfamily Superfamily superfamilyf.14.1 — Voltage-gated ion channels
Family Family familyf.14.1.0 — automated matches
Domain ID domain_idd6vwxf_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.14 — Gated ion channels
Superfamily Superfamily superfamilyf.14.1 — Voltage-gated ion channels
Family Family familyf.14.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id6vwxA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
Domain ID domain_id6vwxD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
Domain ID domain_id6vwxE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
Domain ID domain_id6vwxF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
▶

8. Citations (1)

▶

9. Files and Curves (10)