8P15

Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 2

• PDB DOI: https://doi.org/10.2210/pdb8P15/pdb
• EM Map EMD-17345: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus, Homo sapiens, Mus musculus
• Expression System: Homo sapiens, Escherichia coli BL21(DE3), Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2023-05-11 Released: 2024-11-20 
• Deposition Author(s): Pamula, F., Tejero, O., Muehle, J., Thoma, R., Schertler, G.F.X., Marino, J., Tsai, C.-J.
• Funding Organization(s): Swiss National Science Foundation, European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Characterization of two novel antibody fragments for obtaining cryo-EM structures of GPCR-G protein complexes

Pamula, F., Tejero, O., Muehle, J., Thoma, R., Schertler, G.F.X., Marino, J., Tsai, C.-J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A1B1C1D1E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A2B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 210.33 kDa 
• Atom Count: 12,207 
• Modelled Residue Count: 1,572 
• Deposited Residue Count: 1,898 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A [auth R]	348	Bos taurus	Mutation(s): 3  Gene Names: RHO
UniProt
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	B [auth A]	376	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C [auth B]	340	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P62871 (Bos taurus) Explore P62871  Go to UniProtKB:  P62871

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(T) subunit gamma-T1	D [auth G]	74	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P02698 (Bos taurus) Explore P02698  Go to UniProtKB:  P02698

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
single-chain Fv scFv16	E [auth S]	259	Mus musculus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobin G heavy chain FAB fragment	F [auth H]	262	Mus musculus	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobin G light chain	G [auth L]	239	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1-4487
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Pamula, F., Tejero, O., Muehle, J., Thoma, R., Schertler, G.F.X., Marino, J., Tsai, C.-J.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	173335
Swiss National Science Foundation	Switzerland	153145
Swiss National Science Foundation	Switzerland	192760
European Research Council (ERC)	European Union	951644

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release