Download MendeleyNative mass spectrometry prescreening of G protein-coupled receptor complexes for cryo-EM structure determination
Kim, D.-G., Liu, W., Viner, R., Cherezov, V.To be published.
8VHF
Cryo-EM structure of GPR119-Gs-Nb35 complex with small molecule agonist MBX-2982
- PDB DOI: https://doi.org/10.2210/pdb8VHF/pdb
- EM Map EMD-43236: EMDB EMDataResource
- Classification: MEMBRANE PROTEIN/SIGNALING PROTEIN
- Organism(s): Homo sapiens, Lama glama, Escherichia coli, Oplophorus gracilirostris
- Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2024-01-01 Released: 2024-10-30
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.51 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, HiBiT | A [auth B] | 371 | Homo sapiens | Mutation(s): 0 Gene Names: GNB1 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P62873 (Homo sapiens) Explore P62873 Go to UniProtKB: P62873 | |||||
PHAROS: P62873 GTEx: ENSG00000078369 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P62873 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | B [auth C] | 71 | Homo sapiens | Mutation(s): 0 Gene Names: GNG2 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P59768 (Homo sapiens) Explore P59768 Go to UniProtKB: P59768 | |||||
PHAROS: P59768 GTEx: ENSG00000186469 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P59768 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Nanobody35 | C [auth N] | 138 | Lama glama | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | D [auth A] | 394 | Homo sapiens | Mutation(s): 8 Gene Names: GNAS, GNAS1, GSP EC: 3.6.5 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P63092 (Homo sapiens) Explore P63092 Go to UniProtKB: P63092 | |||||
PHAROS: P63092 GTEx: ENSG00000087460 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P63092 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Soluble cytochrome b562,Glucose-dependent insulinotropic receptor,LgBiT | E [auth R] | 615 | Escherichia coli, Homo sapiens, Oplophorus gracilirostris This entity is chimeric | Mutation(s): 3 Gene Names: cybC, GPR119 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q8TDV5 (Homo sapiens) Explore Q8TDV5 Go to UniProtKB: Q8TDV5 | |||||
PHAROS: Q8TDV5 GTEx: ENSG00000147262 | |||||
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | Q8TDV5P0ABE7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 8VP (Subject of Investigation/LOI) Query on 8VP | F [auth R] | 2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole C22 H24 N8 O S NFTMKHWBOINJGM-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.51 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC | 4.3.1 |
| MODEL REFINEMENT | PHENIX | 1.21rc1_5156: |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-10-30 Deposition Author(s): Kim, D.-G., Cherezov, V.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM127086 |
Revision History (Full details and data files)
- Version 1.0: 2024-10-30
Type: Initial release
