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- EMDB-62665: Structure of mouse C3a bound mouse C3aR in complex with Go -

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Entry
Database: EMDB / ID: EMD-62665
TitleStructure of mouse C3a bound mouse C3aR in complex with Go
Map data
Sample
  • Complex: mouse C3a bound mouse C3aR in complex with Go
    • Complex: mouse C3a anaphylatoxin
      • Protein or peptide: C3a anaphylatoxin
    • Complex: Guanine nucleotide-binding protein G(o) subunit alpha
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: Antibody fragment - ScFv16
      • Protein or peptide: Antibody fragment - ScFv16
    • Complex: mouse C3a anaphylatoxin chemotactic receptor
      • Protein or peptide: Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor
KeywordsGPCR / G protein / SIGNALING PROTEIN / beta-arrestin
Function / homology
Function and homology information


activation of membrane attack complex / Alternative complement activation / classical-complement-pathway C3/C5 convertase complex / oviduct epithelium development / tolerance induction to nonself antigen / Activation of C3 and C5 / complement component C3a binding / cytoplasmic side of Golgi membrane / complement component C3a receptor activity / regulation of complement activation, alternative pathway ...activation of membrane attack complex / Alternative complement activation / classical-complement-pathway C3/C5 convertase complex / oviduct epithelium development / tolerance induction to nonself antigen / Activation of C3 and C5 / complement component C3a binding / cytoplasmic side of Golgi membrane / complement component C3a receptor activity / regulation of complement activation, alternative pathway / vascular associated smooth muscle cell differentiation / positive regulation of opsonization / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / opsonization / Regulation of Complement cascade / positive regulation of type IIa hypersensitivity / Peptide ligand-binding receptors / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / complement component C5a receptor activity / complement activation, lectin pathway / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / positive regulation of activation of membrane attack complex / regulation of complement activation / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / regulation of locomotion / complement-dependent cytotoxicity / G alpha (i) signalling events / positive regulation of glomerular mesangial cell proliferation / serine-type endopeptidase complex / positive regulation of lipid storage / positive regulation of developmental growth / positive regulation of phagocytosis, engulfment / complement activation, GZMK pathway / positive regulation of G protein-coupled receptor signaling pathway / symbiont cell surface / mu-type opioid receptor binding / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / corticotropin-releasing hormone receptor 1 binding / positive regulation of D-glucose transmembrane transport / complement activation / complement receptor mediated signaling pathway / complement activation, alternative pathway / chemokine activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / leukocyte chemotaxis / positive regulation of neutrophil chemotaxis / G protein-coupled dopamine receptor signaling pathway / positive regulation of DNA biosynthetic process / neuron remodeling / endopeptidase inhibitor activity / positive regulation of macrophage chemotaxis / retina development in camera-type eye / parallel fiber to Purkinje cell synapse / amyloid-beta clearance / B cell activation / negative regulation of insulin secretion / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / antigen binding / response to bacterium / postsynaptic modulation of chemical synaptic transmission / Neutrophil degranulation / muscle contraction / positive regulation of smooth muscle cell proliferation / fatty acid metabolic process / positive regulation of phagocytosis / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / calcium-mediated signaling / protein maturation / positive regulation of receptor-mediated endocytosis / positive regulation of protein phosphorylation / regulation of blood pressure / GABA-ergic synapse / chemotaxis / G protein-coupled receptor activity / positive regulation of angiogenesis / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1)
Similarity search - Function
C3a anaphylatoxin chemotactic receptor / Muscarinic acetylcholine receptor M4 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Muscarinic acetylcholine receptor family / Alpha-2-macroglobulin, conserved site ...C3a anaphylatoxin chemotactic receptor / Muscarinic acetylcholine receptor M4 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Muscarinic acetylcholine receptor family / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Formyl peptide receptor-related / : / Alpha-macro-globulin thiol-ester bond-forming region / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Tissue inhibitor of metalloproteinases-like, OB-fold / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
C3a anaphylatoxin chemotactic receptor / Complement C3 / Muscarinic acetylcholine receptor M4 / Guanine nucleotide-binding protein G(o) subunit alpha / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsBanerjee R / Yadav R / Yadav MK / Ganguly M / Mishra S / Dalal A / Gati C / Shukla AK
Funding support India, United Kingdom, 3 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)IPA/2020/000405 India
Wellcome TrustIA/S/20/1/504916 United Kingdom
Science and Engineering Research Board (SERB)CRG/2022/002646 India
CitationJournal: bioRxiv / Year: 2025
Title: Molecular fingerprints of a convergent mechanism orchestrating diverse ligand recognition and species-specific pharmacology at the complement anaphylatoxin receptors.
Authors: Sudha Mishra / Manish K Yadav / Annu Dalal / Manisankar Ganguly / Ravi Yadav / Kazuhiro Sawada / Divyanshu Tiwari / Nabarun Roy / Nilanjana Banerjee / Jenny N Fung / Jianina Marallag / ...Authors: Sudha Mishra / Manish K Yadav / Annu Dalal / Manisankar Ganguly / Ravi Yadav / Kazuhiro Sawada / Divyanshu Tiwari / Nabarun Roy / Nilanjana Banerjee / Jenny N Fung / Jianina Marallag / Cedric S Cui / Xaria X Li / John D Lee / Calvin Aaron Dsouza / Shirsha Saha / Parishmita Sarma / Ganita Rawat / Houming Zhu / Htet A Khant / Richard J Clark / Fumiya K Sano / Ramanuj Banerjee / Trent M Woodruff / Osamu Nureki / Cornelius Gati / Arun K Shukla /
Abstract: Complement anaphylatoxin receptors (C3aR and C5aR1) are prototypical G protein-coupled receptors (GPCRs) playing crucial physiological roles in innate immunity by combating pathogenic infections and ...Complement anaphylatoxin receptors (C3aR and C5aR1) are prototypical G protein-coupled receptors (GPCRs) playing crucial physiological roles in innate immunity by combating pathogenic infections and orchestrating inflammatory responses. They continue to be important therapeutic targets for multiple disorders including autoimmune diseases, acute and chronic inflammation, and allergy-related conditions. Recent structural coverage has provided important insights into their activation and signaling, however, confounding observations in the literature related to ligand efficacy and functional responses, especially in different model systems, present a major challenge for drug discovery efforts. Here, we systematically and comprehensively profile a broad set of natural and synthetic ligands at C3aR and C5aR1 and discover a previously unanticipated level of functional specialization in terms of species-specific pharmacology and receptor activation. Taking a lead from this, we determine seventeen cryo-EM structures of different ligand-receptor-G-protein complexes and uncover distinct orientation of agonists between the human and mouse receptors despite an overlapping positioning in the orthosteric binding pocket. Combined with extensive mutagenesis and functional assays, these structural snapshots allow us to decode and validate a convergent molecular mechanism involving a "Five-Point-Switch" in these receptors that orchestrates the recognition and efficacy of diverse agonists. We also identify species-specific differences at the level of phosphorylation patterns encoded in the carboxyl-terminus of these receptors and directly visualize their impact on βarr binding and activation using cryo-EM structures. Interestingly, we observe that βarrs engage with the mouse C5aR1 using a variation of previously discovered P-X-P-P phosphorylation motif via a "Sliding-Mechanism" and also exhibit distinct oligomeric state for the human vs. mouse receptors. Taken together, this study elucidates functional specialization at the complement anaphylatoxin receptors and underlying molecular mechanisms, offering a previously lacking framework with direct and immediate implications for the development of novel therapeutics.
History
DepositionDec 10, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62665.png

Downloads & links

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Map

FileDownload / File: emd_62665.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 256 pix.
= 331.213 Å		1.29 Å/pix.
x 256 pix.
= 331.213 Å		1.29 Å/pix.
x 256 pix.
= 331.213 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2938 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0611
Minimum - Maximum-0.0415839 - 1.8215344
Average (Standard dev.)0.00053450547 (±0.017544914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 331.2128 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62665_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_62665_half_map_2.map
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Sample components

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Entire : mouse C3a bound mouse C3aR in complex with Go

EntireName: mouse C3a bound mouse C3aR in complex with Go
Components
  • Complex: mouse C3a bound mouse C3aR in complex with Go
    • Complex: mouse C3a anaphylatoxin
      • Protein or peptide: C3a anaphylatoxin
    • Complex: Guanine nucleotide-binding protein G(o) subunit alpha
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: Antibody fragment - ScFv16
      • Protein or peptide: Antibody fragment - ScFv16
    • Complex: mouse C3a anaphylatoxin chemotactic receptor
      • Protein or peptide: Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor

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Supramolecule #1: mouse C3a bound mouse C3aR in complex with Go

SupramoleculeName: mouse C3a bound mouse C3aR in complex with Go / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: mouse C3a anaphylatoxin

SupramoleculeName: mouse C3a anaphylatoxin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Guanine nucleotide-binding protein G(o) subunit alpha

SupramoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: Antibody fragment - ScFv16

SupramoleculeName: Antibody fragment - ScFv16 / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #7: mouse C3a anaphylatoxin chemotactic receptor

SupramoleculeName: mouse C3a anaphylatoxin chemotactic receptor / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Guanine nucleotide-binding protein G(o) subunit alpha

MacromoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.193939 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHEN LYFQGTLSAE ERAALERSKA IEKNLKEDGI SAAKDVKLLL LGADNSGKST IVKQMKIIHG GSGGSGGTTG IVETHFTFK NLHFRLFDVG GQRSERKKWI HCFEDVTAII FCVDLSDYDQ VLHEDETTNR MHESLMLFDS ICNNKFFIDT S IILFLNKK ...String:
MGHHHHHHEN LYFQGTLSAE ERAALERSKA IEKNLKEDGI SAAKDVKLLL LGADNSGKST IVKQMKIIHG GSGGSGGTTG IVETHFTFK NLHFRLFDVG GQRSERKKWI HCFEDVTAII FCVDLSDYDQ VLHEDETTNR MHESLMLFDS ICNNKFFIDT S IILFLNKK DLFGEKIKKS PLTICFPEYT GPNTYEDAAA YIQAQFESKN RSPNKEIYCH MTCATDTNNA QVIFDAVTDI II ANNLRGC GLY

UniProtKB: Guanine nucleotide-binding protein G(o) subunit alpha, Guanine nucleotide-binding protein G(o) subunit alpha

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.534062 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV ...String:
MHHHHHHGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV TSSGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD IN AICFFPN GNAFATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAG HDNRVS CLGVTDDGMA VATGSWDSFL KIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: C3a anaphylatoxin

MacromoleculeName: C3a anaphylatoxin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.431053 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GKSVQLMERR MDKAGQYTDK GLRKCCEDGM RDIPMRYSCQ RRARLITQGE NCIKAFIDCC NHITKLREQH RRDHVLGLAR

UniProtKB: Complement C3

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Macromolecule #4: Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotacti...

MacromoleculeName: Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 59.526031 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSESF DADTNSTDLH SRPLFQPQDI ASMVILGLT CLLGLLGNGL VLWVAGVKMK TTVNTVWFLH LTLADFLCCL SLPFSLAHLI LQGHWPYGLF LCKLIPSIII L NMFASVFL ...String:
MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSESF DADTNSTDLH SRPLFQPQDI ASMVILGLT CLLGLLGNGL VLWVAGVKMK TTVNTVWFLH LTLADFLCCL SLPFSLAHLI LQGHWPYGLF LCKLIPSIII L NMFASVFL LTAISLDRCL IVHKPIWCQN HRNVRTAFAI CGCVWVVAFV MCVPVFVYRD LFIMDNRSIC RYNFDSSRSY DY WDYVYKL SLPESNSTDN STAQLTGHMN DRSAPSSVQA RDYFWTVTTA LQSQPFLTSP EDSFSLDSAN QQPHYGGKPP NVL TAAVPS GFPVEDRKSN TLNADAFLSA HTELFPTASS GHLYPYDFQG DYVDQFTYDN HVPTPLMAIT ITRLVVGFLV PFFI MVICY SLIVFRMRKT NFTKSRNKTF RVAVAVVTVF FICWTPYHLV GVLLLITDPE SSLGEAVMSW DHMSIALASA NSCFN PFLY ALLGKDFRKK ARQSIKGILE AAFSEELTHS TNCTQDKASS KRNNMSTDV

UniProtKB: Muscarinic acetylcholine receptor M4, C3a anaphylatoxin chemotactic receptor

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Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #6: Antibody fragment - ScFv16

MacromoleculeName: Antibody fragment - ScFv16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.466486 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL K

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9kv6

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 175697
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9kv6


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9kzk:
Structure of mouse C3a bound mouse C3aR in complex with Go

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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