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- EMDB-34943: Structure of C5a-pep bound mouse C5aR1 in complex with Go -

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Entry
Database: EMDB / ID: EMD-34943
TitleStructure of C5a-pep bound mouse C5aR1 in complex with Go
Map data
Sample
  • Complex: GPCR-G protein in complex with a synthetic peptide agonist
    • Complex: C5a anaphylatoxin chemotactic receptor 1
      • Protein or peptide: C5a anaphylatoxin chemotactic receptor 1
    • Complex: synthetic peptidePeptide synthesis
      • Protein or peptide: MEA-LYS-PRO-ZAL-ALC-DAR
    • 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(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • 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: Antibody fragment
      • Protein or peptide: Antibody fragment ScFv16
KeywordsGPCR / G protein / SIGNALING PROTEIN / SIGNATLING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


complement component C5a binding / cell proliferation in hindbrain / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / Peptide ligand-binding receptors / complement component C5a receptor activity / Regulation of Complement cascade / response to peptidoglycan / G alpha (i) signalling events ...complement component C5a binding / cell proliferation in hindbrain / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / Peptide ligand-binding receptors / complement component C5a receptor activity / Regulation of Complement cascade / response to peptidoglycan / G alpha (i) signalling events / mu-type opioid receptor binding / complement receptor mediated signaling pathway / corticotropin-releasing hormone receptor 1 binding / positive regulation of neutrophil chemotaxis / dopamine receptor signaling pathway / positive regulation of macrophage chemotaxis / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / G protein-coupled serotonin receptor binding / Neutrophil degranulation / neutrophil chemotaxis / muscle contraction / G protein-coupled receptor activity / positive regulation of epithelial cell proliferation / astrocyte activation / microglial cell activation / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / mRNA transcription by RNA polymerase II / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / cognition / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / positive regulation of angiogenesis / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / apical part of cell / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / cytoplasmic vesicle / G alpha (s) signalling events / G alpha (q) signalling events / basolateral plasma membrane / negative regulation of neuron apoptotic process / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / GTP binding / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. ...Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(o) subunit alpha / C5a anaphylatoxin chemotactic receptor 1 / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsSaha S / Maharana J / Yadav MK / Sarma P / Chami M / Banerjee R / Shukla AK
Funding support India, 1 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR29041/BRB/10/1697/20 India
CitationJournal: Cell(Cambridge,Mass.) / Year: 2023
Title: Structure of a GPCR-G protein in complex with a synthetic peptide agonist
Authors: Saha S / Maharana J / Yadav MK / Sarma P / Chami M / Banerjee R / Shukla AK
History
DepositionDec 13, 2022-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34943.png

Downloads & links

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Map

FileDownload / File: emd_34943.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.94756 Å
Density
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.325697 - 1.7367756
Average (Standard dev.)0.0004159261 (±0.024090977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 341.1216 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34943_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34943_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPCR-G protein in complex with a synthetic peptide agonist

EntireName: GPCR-G protein in complex with a synthetic peptide agonist
Components
  • Complex: GPCR-G protein in complex with a synthetic peptide agonist
    • Complex: C5a anaphylatoxin chemotactic receptor 1
      • Protein or peptide: C5a anaphylatoxin chemotactic receptor 1
    • Complex: synthetic peptidePeptide synthesis
      • Protein or peptide: MEA-LYS-PRO-ZAL-ALC-DAR
    • 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(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • 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: Antibody fragment
      • Protein or peptide: Antibody fragment ScFv16

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Supramolecule #1: GPCR-G protein in complex with a synthetic peptide agonist

SupramoleculeName: GPCR-G protein in complex with a synthetic peptide agonist
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: C5a anaphylatoxin chemotactic receptor 1

SupramoleculeName: C5a anaphylatoxin chemotactic receptor 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: synthetic peptide

SupramoleculeName: synthetic peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Chemically synthesized peptide fragment derived from the C-terminus of human C5a.

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Supramolecule #4: Guanine nucleotide-binding protein G(o) subunit alpha

SupramoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Details: This is a variant of Guanine nucleotide-binding protein G(o) subunit alpha (Uniprot ID: P09471) called the "mini G(o) alpha"
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: #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: 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: 6 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: Antibody fragment

SupramoleculeName: Antibody fragment / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #6
Details: Single Chain Variable Fragment of an antibody referred to as ScFv16
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: C5a anaphylatoxin chemotactic receptor 1

MacromoleculeName: C5a anaphylatoxin chemotactic receptor 1 / type: protein_or_peptide / ID: 1
Details: The initial sequence in the sample sequence is the expression tag (absent in the coordinates): "MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDPIDNSSFEINYDHYGTMDPNIPADGIHLPKRQP" ...Details: The initial sequence in the sample sequence is the expression tag (absent in the coordinates): "MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDPIDNSSFEINYDHYGTMDPNIPADGIHLPKRQP" The residues missing in the coordinates as compared to the sample sequence are the residues with disorder.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 44.958422 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSDPI DNSSFEINYD HYGTMDPNIP ADGIHLPKR QPGDVAALII YSVVFLVGVP GNALVVWVTA FEARRAVNAI WFLNLAVADL LSCLALPVLF TTVLNHNYWY F DATACIVL ...String:
MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSDPI DNSSFEINYD HYGTMDPNIP ADGIHLPKR QPGDVAALII YSVVFLVGVP GNALVVWVTA FEARRAVNAI WFLNLAVADL LSCLALPVLF TTVLNHNYWY F DATACIVL PSLILLNMYA SILLLATISA DRFLLVFKPI WCQKVRGTGL AWMACGVAWV LALLLTIPSF VYREAYKDFY SE HTVCGIN YGGGSFPKEK AVAILRLMVG FVLPLLTLNI CYTFLLLRTW SRKATRSTKT LKVVMAVVIC FFIFWLPYQV TGV MIAWLP PSSPTLKRVE KLNSLCVSLA YINCCVNPII YVMAGQGFHG RLLRSLPSII RNALSEDSVG RDSKTFTPST TDTS TRKSQ AV

UniProtKB: C5a anaphylatoxin chemotactic receptor 1

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Macromolecule #2: MEA-LYS-PRO-ZAL-ALC-DAR

MacromoleculeName: MEA-LYS-PRO-ZAL-ALC-DAR / type: protein_or_peptide / ID: 2
Details: This is a chemically synthesized peptide derived from the C-terminus of human C5a.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 869.148 Da
SequenceString:
(MEA)KP(ZAL)(ALC)(DAR)

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

MacromoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: protein_or_peptide / ID: 3
Details: This is a variant of Guanine nucleotide-binding protein G(o) subunit alpha (Uniprot ID: P09471) called the "mini G(o) alpha";The initial sequence in the provided sample sequence is the ...Details: This is a variant of Guanine nucleotide-binding protein G(o) subunit alpha (Uniprot ID: P09471) called the "mini G(o) alpha";The initial sequence in the provided sample sequence is the expression tag: "MGHHHHHHENLYFQGT",This is a variant of Guanine nucleotide-binding protein G(o) subunit alpha (Uniprot ID: P09471) called the "mini G(o) alpha";The initial sequence in the provided sample sequence is the expression tag: "MGHHHHHHENLYFQGT"
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.024762 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHEN LYFQGTLSAE ERAALERSKA IEKNLKEDGI SAAKDVKLLL LGADNSGKST IVKQMKIIHG GSGGSGGTTG IVETHFTFK NLHFRLFDVG GQRSERKKWI HCFEDVTAII FCVDLSDYNR MHESLMLFDS ICNNKFFIDT SIILFLNKKD L FGEKIKKS ...String:
MGHHHHHHEN LYFQGTLSAE ERAALERSKA IEKNLKEDGI SAAKDVKLLL LGADNSGKST IVKQMKIIHG GSGGSGGTTG IVETHFTFK NLHFRLFDVG GQRSERKKWI HCFEDVTAII FCVDLSDYNR MHESLMLFDS ICNNKFFIDT SIILFLNKKD L FGEKIKKS PLTICFPEYT GPNTYEDAAA YIQAQFESKN RSPNKEIYCH MTCATDTNNA QVIFDAVTDI IIANNLRGCG LY

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

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Macromolecule #4: 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: 4
Details: The initial sequence present in the sample sequence and absent in the coordinates is the expression tag: "MHHHHHHGSSGS"
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.198656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF LDDNQIVTSS G DTTCALWD ...String:
ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF LDDNQIVTSS G DTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TFTGHESDIN AICFFPNGNA FA TGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKADRAGVLA GHDNRVSCLG VTD DGMAVA TGSWDSFLKI WN

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

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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
Details: The missing residues in the coordinates are the regions which are disordered.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.160126 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASIAQARKLV EQLKMEANID RIKVSKAAAD LMAYCEAHAK EDPLLTPVPA SENPFR

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
Details: The residues absent in the coordinates are the regions which are disordered.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.340482 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 KGSLEVLFQ

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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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7wvv

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 380463
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8hpt:
Structure of C5a-pep bound mouse C5aR1 in complex with Go

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