7RKY

Binding mode of US27-Gi-scFv16 in OCL-state

• PDB DOI: https://doi.org/10.2210/pdb7RKY/pdb
• EM Map EMD-24507: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus, Human betaherpesvirus 5
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2021-07-22 Released: 2022-01-26 
• Deposition Author(s): Tsutsumi, N., Jude, K.M., Garcia, K.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins

Tsutsumi, N., Maeda, S., Qu, Q., Voegele, M., Jude, K.M., Suomivuori, C.M., Panova, O., Waghray, D., Kato, H.E., Velasco, A., Dror, R.O., Skiniotis, G., Kobilka, B.K., Garcia, K.C.

(2022) Sci Adv 8: eabl5442

• DOI: https://doi.org/10.1126/sciadv.abl5442

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 157.68 kDa 
• Atom Count: 8,894 
• Modelled Residue Count: 1,219 
• Deposited Residue Count: 1,403 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	353	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	345	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	67	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody fragment scFv16	D	256	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor homolog US27	E [auth R]	382	Human betaherpesvirus 5	Mutation(s): 0  Gene Names: US27 Membrane Entity: Yes
UniProt
Find proteins for P09703 (Human cytomegalovirus (strain AD169)) Explore P09703  Go to UniProtKB:  P09703

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	F [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Tsutsumi, N., Jude, K.M., Garcia, K.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI125320
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release