8JZP | pdb_00008jzp

Structure of mouse C5a-human C5aR1-Go complex

• PDB DOI: https://doi.org/10.2210/pdb8JZP/pdb
• EM Map EMD-36750: EMDB EMDataResource

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


• Deposited: 2023-07-06 Released: 2025-01-15 
• Deposition Author(s): Yadav, M.K., Yadav, R., Maharana, J., Sarma, P., Banerjee, R., Shukla, A.K., Gati, C.
• Funding Organization(s): Department of Biotechnology (DBT, India), Wellcome Trust, Science and Engineering Research Board (SERB)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structure of mouse C5a-human C5aR1-Go complex

Yadav, M.K., Yadav, R., Maharana, J., Sarma, P., Banerjee, R., Shukla, A.K., Gati, C.

To be published.

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: 157.92 kDa 
• Atom Count: 8,622 
• Modeled Residue Count: 1,199 
• Deposited Residue Count: 1,424 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C5a anaphylatoxin chemotactic receptor 1	A	406	Homo sapiens	Mutation(s): 0  Gene Names: C5AR1, C5AR, C5R1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P21730 (Homo sapiens) Explore P21730  Go to UniProtKB:  P21730
PHAROS:  P21730 GTEx:  ENSG00000197405

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(o) subunit alpha	B	240	Homo sapiens	Mutation(s): 6  Gene Names: GNAO1 EC: 3.6.5 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	350	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
C5a anaphylatoxin	D [auth F]	109	Mus musculus	Mutation(s): 0  Gene Names: C5, Hc Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P06684 (Mus musculus) Explore P06684  Go to UniProtKB:  P06684
IMPC:  MGI:96031

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]	71	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]	248	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Yadav, M.K., Yadav, R., Maharana, J., Sarma, P., Banerjee, R., Shukla, A.K., Gati, C.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR29041/BRB/10/1697/2018
Wellcome Trust	United Kingdom	IA/S/20/1/504916
Science and Engineering Research Board (SERB)	India	SPR/2020/000408
Science and Engineering Research Board (SERB)	India	IPA/2020/000405

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release