8HPT

Structure of C5a-pep bound mouse C5aR1 in complex with Go

• PDB DOI: https://doi.org/10.2210/pdb8HPT/pdb
• EM Map EMD-34943: EMDB EMDataResource

• Classification: SIGNATLING PROTEIN/IMMUNE SYSTEM
• Organism(s): Mus musculus, synthetic construct, Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2022-12-13 Released: 2023-10-18 
• Deposition Author(s): Saha, S., Maharana, J., Yadav, M.K., Sarma, P., Chami, M., Banerjee, R., Shukla, A.K.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of a GPCR-G protein in complex with a synthetic peptide agonist

Saha, S., Maharana, J., Yadav, M.K., Sarma, P., Chami, M., Banerjee, R., Shukla, A.K.

(2023) Cell 

• DOI: https://doi.org/https://doi.org/10.1016/j.cell.2023.09.020

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 143.55 kDa 
• Atom Count: 7,897 
• Modelled Residue Count: 1,095 
• Deposited Residue Count: 1,303 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C5a anaphylatoxin chemotactic receptor 1	A	407	Mus musculus	Mutation(s): 0  Gene Names: C5ar1, C5ar, C5r1 Membrane Entity: Yes
UniProt
Find proteins for P30993 (Mus musculus) Explore P30993  Go to UniProtKB:  P30993

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MEA-LYS-PRO-ZAL-ALC-DAR	B [auth D]	6	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(o) subunit alpha	C [auth B]	240	Homo sapiens	Mutation(s): 6  Gene Names: GNAO1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P09471 (Homo sapiens) Explore P09471  Go to UniProtKB:  P09471
PHAROS:  P09471 GTEx:  ENSG00000087258

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth C]	338	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth G]	56	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody fragment ScFv16	F [auth H]	256	Mus musculus	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALC	B [auth D]	L-PEPTIDE LINKING	C9 H17 N O2		ALA
MEA	B [auth D]	L-PEPTIDE LINKING	C10 H13 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Saha, S., Maharana, J., Yadav, M.K., Sarma, P., Chami, M., Banerjee, R., Shukla, A.K.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR29041/BRB/10/1697/20

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Data collection