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- EMDB-38539: Cryo-EM structure of the tethered agonist-bound human PAR1-Gi complex -

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Entry
Database: EMDB / ID: EMD-38539
TitleCryo-EM structure of the tethered agonist-bound human PAR1-Gi complex
Map data
Sample
  • Complex: tethered agonist-bound human PAR1-Gi complex
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: 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(O) subunit gamma-2
    • Protein or peptide: scFv16
    • Protein or peptide: Proteinase-activated receptor 1 LgBiT
  • Ligand: CHOLESTEROL
KeywordsGPCR / MEMBRANE PROTEIN / protease-activated receptor
Function / homology
Function and homology information


negative regulation of renin secretion into blood stream / negative regulation of glomerular filtration / dendritic cell homeostasis / establishment of synaptic specificity at neuromuscular junction / thrombin-activated receptor signaling pathway / thrombin-activated receptor activity / platelet dense tubular network / cell-cell junction maintenance / regulation of interleukin-1 beta production / platelet dense granule organization ...negative regulation of renin secretion into blood stream / negative regulation of glomerular filtration / dendritic cell homeostasis / establishment of synaptic specificity at neuromuscular junction / thrombin-activated receptor signaling pathway / thrombin-activated receptor activity / platelet dense tubular network / cell-cell junction maintenance / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of sensory perception of pain / positive regulation of smooth muscle contraction / positive regulation of calcium ion transport / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / : / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (i) signalling events / alkylglycerophosphoethanolamine phosphodiesterase activity / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / photoreceptor outer segment membrane / positive regulation of Rho protein signal transduction / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (i) signalling events / spectrin binding / Vasopressin regulates renal water homeostasis via Aquaporins / : / regulation of blood coagulation / photoreceptor outer segment / positive regulation of collagen biosynthetic process / G-protein alpha-subunit binding / anatomical structure morphogenesis / T cell migration / D2 dopamine receptor binding / positive regulation of blood coagulation / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / Common Pathway of Fibrin Clot Formation / G protein-coupled serotonin receptor binding / cellular response to forskolin / positive regulation of vasoconstriction / regulation of mitotic spindle organization / homeostasis of number of cells within a tissue / cardiac muscle cell apoptotic process / release of sequestered calcium ion into cytosol / photoreceptor inner segment / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / positive regulation of GTPase activity / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of interleukin-8 production / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / positive regulation of receptor signaling pathway via JAK-STAT / neuromuscular junction / G-protein beta/gamma-subunit complex binding / caveola / regulation of synaptic plasticity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / :
Similarity search - Function
Thrombin receptor / Protease-activated receptor / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. ...Thrombin receptor / Protease-activated receptor / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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 / 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
Proteinase-activated receptor 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus (rat) / Bos taurus (cattle) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGuo J / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2024
Title: Structural basis of tethered agonism and G protein coupling of protease-activated receptors.
Authors: Jia Guo / Yun-Li Zhou / Yixin Yang / Shimeng Guo / Erli You / Xin Xie / Yi Jiang / Chunyou Mao / H Eric Xu / Yan Zhang /
Abstract: Protease-activated receptors (PARs) are a unique group within the G protein-coupled receptor superfamily, orchestrating cellular responses to extracellular proteases via enzymatic cleavage, which ...Protease-activated receptors (PARs) are a unique group within the G protein-coupled receptor superfamily, orchestrating cellular responses to extracellular proteases via enzymatic cleavage, which triggers intracellular signaling pathways. Protease-activated receptor 1 (PAR1) is a key member of this family and is recognized as a critical pharmacological target for managing thrombotic disorders. In this study, we present cryo-electron microscopy structures of PAR1 in its activated state, induced by its natural tethered agonist (TA), in complex with two distinct downstream proteins, the G and G heterotrimers, respectively. The TA peptide is positioned within a surface pocket, prompting PAR1 activation through notable conformational shifts. Contrary to the typical receptor activation that involves the outward movement of transmembrane helix 6 (TM6), PAR1 activation is characterized by the simultaneous downward shift of TM6 and TM7, coupled with the rotation of a group of aromatic residues. This results in the displacement of an intracellular anion, creating space for downstream G protein binding. Our findings delineate the TA recognition pattern and highlight a distinct role of the second extracellular loop in forming β-sheets with TA within the PAR family, a feature not observed in other TA-activated receptors. Moreover, the nuanced differences in the interactions between intracellular loops 2/3 and the Gα subunit of different G proteins are crucial for determining the specificity of G protein coupling. These insights contribute to our understanding of the ligand binding and activation mechanisms of PARs, illuminating the basis for PAR1's versatility in G protein coupling.
History
DepositionJan 2, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38539.png

Downloads & links

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Map

FileDownload / File: emd_38539.map.gz / Format: CCP4 / Size: 30.5 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.)
1.07 Å/pix.
x 200 pix.
= 214.2 Å		1.07 Å/pix.
x 200 pix.
= 214.2 Å		1.07 Å/pix.
x 200 pix.
= 214.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0207
Minimum - Maximum-0.0375352 - 0.094304375
Average (Standard dev.)-0.000093131945 (±0.0035921934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38539_half_map_1.map
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Half map: #2

Fileemd_38539_half_map_2.map
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Sample components

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Entire : tethered agonist-bound human PAR1-Gi complex

EntireName: tethered agonist-bound human PAR1-Gi complex
Components
  • Complex: tethered agonist-bound human PAR1-Gi complex
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: 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(O) subunit gamma-2
    • Protein or peptide: scFv16
    • Protein or peptide: Proteinase-activated receptor 1 LgBiT
  • Ligand: CHOLESTEROL

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Supramolecule #1: tethered agonist-bound human PAR1-Gi complex

SupramoleculeName: tethered agonist-bound human PAR1-Gi complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.313863 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GCTLSAEDKA AVERSKMIDR NLREDGEKAA REVKLLLLGA GESGKSTIVK QMKIIHEAGY SEEECKQYKA VVYSNTIQSI IAIIRAMGR LKIDFGDSAR ADDARQLFVL AGAAEEGFMT AELAGVIKRL WKDSGVQACF NRSREYQLND SAAYYLNDLD R IAQPNYIP ...String:
GCTLSAEDKA AVERSKMIDR NLREDGEKAA REVKLLLLGA GESGKSTIVK QMKIIHEAGY SEEECKQYKA VVYSNTIQSI IAIIRAMGR LKIDFGDSAR ADDARQLFVL AGAAEEGFMT AELAGVIKRL WKDSGVQACF NRSREYQLND SAAYYLNDLD R IAQPNYIP TQQDVLRTRV KTTGIVETHF TFKDLHFKMF DVGAQRSERK KWIHCFEGVT AIIFCVALSD YDLVLAEDEE MN RMHESMK LFDSICNNKW FTDTSIILFL NKKDLFEEKI KKSPLTICYP EYAGSNTYEE AAAYIQCQFE DLNKRKDTKE IYT HFTCST DTKNVQFVFD AVTDVIIKNN LKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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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: Rattus (rat)
Molecular weightTheoretical: 41.332137 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSGWRLFKK ISGSSGGGGS GGGGSSGGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKI YAMHWGTDSR LLVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT R EGNVRVSR ...String:
MVSGWRLFKK ISGSSGGGGS GGGGSSGGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKI YAMHWGTDSR LLVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT R EGNVRVSR ELAGHTGYLS CCRFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AK LWDVREG MCRQTFTGHE SDINAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGY DDFNCN VWDALKADRA GVLAGHDNRV SCLGVTDDGM AVATGSWDSF LKIWNHHHHH HHH

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

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 7.432554 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFC

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

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Macromolecule #4: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 40.523266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LLVNQSHQGF NKEHTSKMVS AIVLYVLLAA AAHSAFAVQL VESGGGLVQP GGSRKLSCSA SGFAFSSFGM HWVRQAPEKG LEWVAYISS GSGTIYYADT VKGRFTISRD DPKNTLFLQM TSLRSEDTAM YYCVRSIYYY GSSPFDFWGQ GTTLTVSAGG G GSGGGGSG ...String:
LLVNQSHQGF NKEHTSKMVS AIVLYVLLAA AAHSAFAVQL VESGGGLVQP GGSRKLSCSA SGFAFSSFGM HWVRQAPEKG LEWVAYISS GSGTIYYADT VKGRFTISRD DPKNTLFLQM TSLRSEDTAM YYCVRSIYYY GSSPFDFWGQ GTTLTVSAGG G GSGGGGSG GGGSADIVMT QATSSVPVTP GESVSISCRS SKSLLHSNGN TYLYWFLQRP GQSPQLLIYR MSNLASGVPD RF SGSGSGT AFTLTISRLE AEDVGVYYCM QHLEYPLTFG AGTKLELVDE NLYFQGASHH HHHHHHWFLQ RPGQSPQLLI YRM SNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FGAGTKLEL

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Macromolecule #5: Proteinase-activated receptor 1 LgBiT

MacromoleculeName: Proteinase-activated receptor 1 LgBiT / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.787539 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SFLLRNPNDK YEPFWEDEEK NESGLTEYRL VSINKSSPLQ KQLPAFISED ASGYLTSSWL TLFVPSVYTG VFVVSLPLNI MAIVVFILK MKVKKPAVVY MLHLATADVL FVSVLPFKIS YYFSGSDWQF GSELCRFVTA AFYCNMYASI LLMTVISIDR F LAVVYPMQ ...String:
SFLLRNPNDK YEPFWEDEEK NESGLTEYRL VSINKSSPLQ KQLPAFISED ASGYLTSSWL TLFVPSVYTG VFVVSLPLNI MAIVVFILK MKVKKPAVVY MLHLATADVL FVSVLPFKIS YYFSGSDWQF GSELCRFVTA AFYCNMYASI LLMTVISIDR F LAVVYPMQ SLSWRTLGRA SFTCLAIWAL AIAGVVPLLL KEQTIQVPGL NITTCHDVLN ETLLEGYYAY YFSAFSAVFF FV PLIISTV CYVSIIRCLS SSAVANRSKK SRALFLSAAV FCIFIICFGP TNVLLIAHYS FLSHTSTTEA AYFAYLLCVC VSS ISCCID PLIYYYASSE CQRYVYSILC CKESSDPSSY GSSGGGGSGG GGSSGVFTLE DFVGDWEQTA AYNLDQVLEQ GGVS SLLQN LAVSVTPIQR IVRSGENALK IDIHVIIPYE GLSADQMAQI EEVFKVVYPV DDHHFKVILP YGTLVIDGVT PNMLN YFGR PYEGIAVFDG KKITVTGTLW NGNKIIDERL ITPDGSMLFR VTINSGGS

UniProtKB: Proteinase-activated receptor 1

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
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:

3vw7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162724
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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