Download MendeleyAn extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking
Dey, D., Singh, S., Khan, S., Martin, M., Schnicker, N.J., Gakhar, L., Pierce, B.G., Hasan, S.S.(2022) Commun Biol 5: 115
7S16 | pdb_00007s16
Crystal structure of alpha-COP-WD40 domain R57A mutant
- PDB DOI: https://doi.org/10.2210/pdb7S16/pdb
- Classification: PROTEIN TRANSPORT
- Organism(s): Schizosaccharomyces pombe
- Expression System: Homo sapiens
- Mutation(s): Yes
- Deposited: 2021-09-01 Released: 2022-02-16
- Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.24 Å
- R-Value Free: 0.159 (Depositor), 0.160 (DCC)
- R-Value Work: 0.135 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.136 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Coatomer subunit alpha | 338 | Schizosaccharomyces pombe | Mutation(s): 2 |  | |
UniProt | |||||
Find proteins for Q96WV5 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q96WV5 Go to UniProtKB: Q96WV5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q96WV5 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NA Query on NA | B [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.24 Å
- R-Value Free: 0.159 (Depositor), 0.160 (DCC)
- R-Value Work: 0.135 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.136 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 35.868 | α = 90 |
| b = 56.712 | β = 99.37 |
| c = 70.548 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-02-16 Deposition Author(s): Dey, D., Singh, S., Khan, S., Martin, M., Schnicker, N., Gakhar, L., Pierce, B., Hasan, S.S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | P30CA134274 |
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | P30CA086862 |
Revision History (Full details and data files)
- Version 1.0: 2022-02-16
Type: Initial release - Version 1.1: 2022-03-02
Changes: Author supporting evidence - Version 1.2: 2023-10-18
Changes: Data collection, Refinement description - Version 1.3: 2024-11-20
Changes: Structure summary
