6A91
Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana bound with saxitoxin and Dc1a
- PDB DOI: https://doi.org/10.2210/pdb6A91/pdb
- EM Map EMD-6996: EMDB EMDataResource
- Classification: MEMBRANE PROTEIN/TOXIN
- Organism(s): Periplaneta americana, Diguetia canities
- Expression System: Homo sapiens, Escherichia coli
- Mutation(s): No
- Membrane Protein: Yes PDBTMMemProtMDmpstruc
- Deposited: 2018-07-11 Released: 2018-08-08
- Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China, Australian Research Council, National Health and Medical Research Council (Australia)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.20 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 2.0 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Sodium channel protein PaFPC1 | 1,596 | Periplaneta americana | Mutation(s): 0 Membrane Entity: Yes |  | |
UniProt | |||||
Find proteins for D0E0C2 (Periplaneta americana) Explore D0E0C2 Go to UniProtKB: D0E0C2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D0E0C2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Mu-diguetoxin-Dc1a | 57 | Diguetia canities | Mutation(s): 0 Membrane Entity: Yes |  | |
UniProt | |||||
Find proteins for P49126 (Diguetia canities) Explore P49126 Go to UniProtKB: P49126 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P49126 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PC1 Query on PC1 | H [auth A], I [auth A] | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N |  | ||
| 9SL Query on 9SL | J [auth A] | [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate C10 H17 N7 O4 RPQXVSUAYFXFJA-HGRQIUPRSA-N |  | ||
| NAG Query on NAG | E [auth A], F [auth A], G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.20 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | RELION | 2.1 |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-08-08 Deposition Author(s): Shen, H.Z., li, Z.Q., Jiang, Y., Pan, X.J., Wu, J.P., Cristofori-Armstrong, B., Smith, J.J., Chin, Y.K.Y., Lei, J.L., Zhou, Q., King, G.F., Yan, N.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Ministry of Science and Technology (China) | China | 2015CB910101 |
| Ministry of Science and Technology (China) | China | 2016YFA0500402 |
| National Natural Science Foundation of China | China | 31621092 |
| National Natural Science Foundation of China | China | 31630017 |
| National Natural Science Foundation of China | China | 31611130036 |
| Australian Research Council | Australia | DP160104411 |
| National Health and Medical Research Council (Australia) | Australia | APP1072113 |
Revision History (Full details and data files)
- Version 1.0: 2018-08-08
Type: Initial release - Version 1.1: 2018-12-26
Changes: Data collection, Database references - Version 1.2: 2019-11-06
Changes: Data collection, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
