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- EMDB-63832: Cryo-EM structure of D-peptide-GPCR-Gq complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63832
TitleCryo-EM structure of D-peptide-GPCR-Gq complex
Map dataGlobal electron density of complex
Sample
  • Complex: V1aR(D112K) with Gq
    • Protein or peptide: exo-alpha-sialidase,Vasopressin V1a receptor
    • Protein or peptide: Arg-vasopressin
    • Protein or peptide: Guanine nucleotide-binding protein G(q) 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: Nanobody 35
KeywordsGPCR / vasopressin / complex / SIGNALING PROTEIN/IMMUNE SYSTEM / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


V1B vasopressin receptor binding / : / Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / V1A vasopressin receptor binding / negative regulation of female receptivity / cellular response to water deprivation / neurohypophyseal hormone activity / response to nerve growth factor / maternal aggressive behavior / negative regulation of transmission of nerve impulse ...V1B vasopressin receptor binding / : / Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / V1A vasopressin receptor binding / negative regulation of female receptivity / cellular response to water deprivation / neurohypophyseal hormone activity / response to nerve growth factor / maternal aggressive behavior / negative regulation of transmission of nerve impulse / Organic anion transport by SLCO transporters / myotube differentiation / grooming behavior / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / sperm ejaculation / regulation of systemic arterial blood pressure by vasopressin / Vasopressin-like receptors / renal water absorption / vasopressin receptor activity / response to peptide / response to 2,3,7,8-tetrachlorodibenzodioxine / telencephalon development / vasoconstriction / positive regulation of prostaglandin biosynthetic process / maternal behavior / water transport / ganglioside catabolic process / neuropeptide hormone activity / oligosaccharide catabolic process / blood circulation / response to corticosterone / positive regulation of glutamate secretion / exo-alpha-sialidase / positive regulation of systemic arterial blood pressure / exo-alpha-sialidase activity / response to testosterone / peptide hormone binding / social behavior / response to electrical stimulus / response to salt stress / multicellular organismal response to stress / positive regulation of vasoconstriction / endocytic vesicle / positive regulation of heart rate / neuronal dense core vesicle / cellular response to hormone stimulus / transport across blood-brain barrier / BMAL1:CLOCK,NPAS2 activates circadian expression / secretory granule / hormone activity / locomotory behavior / protein kinase C binding / calcium-mediated signaling / response to nicotine / generation of precursor metabolites and energy / clathrin-coated endocytic vesicle membrane / 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) / photoreceptor disc membrane / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / cell-cell signaling / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / positive regulation of cell growth / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / Cargo recognition for clathrin-mediated endocytosis / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / Clathrin-mediated endocytosis / G-protein beta-subunit binding / extracellular vesicle / positive regulation of cytosolic calcium ion concentration / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / GTPase binding / Ca2+ pathway
Similarity search - Function
Vasopressin V1A receptor / Vasopressin V1 receptor, C-terminal / Vasopressin V1 receptor, C-terminal / DUF1856 / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones signature. ...Vasopressin V1A receptor / Vasopressin V1 receptor, C-terminal / Vasopressin V1 receptor, C-terminal / DUF1856 / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones / BNR repeat-like domain / Vasopressin receptor / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / Sialidase family / Sialidase / Sialidase superfamily / 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 WD-40 repeat protein / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / Concanavalin A-like lectin/glucanase domain superfamily / 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
Similarity search - Domain/homology
Vasopressin-neurophysin 2-copeptin / Vasopressin V1a receptor / 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 / exo-alpha-sialidase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsLiu SH / Zhang YJ / Hua T / Liu ZJ
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: Cryo-EM structure of D-peptide-GPCR-Gq complex
Authors: Liu SH / Zhang YJ / Hua T / Liu ZJ
History
DepositionMar 19, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63832.png

Downloads & links

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Map

FileDownload / File: emd_63832.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal electron density of complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017793697 - 2.2556417
Average (Standard dev.)0.0008839779 (±0.022352908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63832_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The electron density subjected to local refinement focusing...

Fileemd_63832_additional_1.map
AnnotationThe electron density subjected to local refinement focusing on the GPCR receptor (R chain) and the Galpha subunit (A chain).
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63832_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63832_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : V1aR(D112K) with Gq

EntireName: V1aR(D112K) with Gq
Components
  • Complex: V1aR(D112K) with Gq
    • Protein or peptide: exo-alpha-sialidase,Vasopressin V1a receptor
    • Protein or peptide: Arg-vasopressin
    • Protein or peptide: Guanine nucleotide-binding protein G(q) 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: Nanobody 35

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Supramolecule #1: V1aR(D112K) with Gq

SupramoleculeName: V1aR(D112K) with Gq / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: exo-alpha-sialidase,Vasopressin V1a receptor

MacromoleculeName: exo-alpha-sialidase,Vasopressin V1a receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.958078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAGRAVEG AVKTEPVDLF HPGFLNSSNY RIPALFKTKE GTLIASIDAR RHGGADAPNN DIDTAVRRS EDGGKTWDEG QIIMDYPDKS SVIDTTLIQD DETGRIFLLV THFPSKYGFW NAGLGSGFKN IDGKEYLCLY D SSGKEFTV ...String:
MKTIIALSYI FCLVFADYKD DDDAGRAVEG AVKTEPVDLF HPGFLNSSNY RIPALFKTKE GTLIASIDAR RHGGADAPNN DIDTAVRRS EDGGKTWDEG QIIMDYPDKS SVIDTTLIQD DETGRIFLLV THFPSKYGFW NAGLGSGFKN IDGKEYLCLY D SSGKEFTV RENVVYDKDS NKTEYTTNAL GDLFKNGTKI DNINSSTAPL KAKGTSYINL VYSDDDGKTW SEPQNINFQV KK DWMKFLG IAPGRGIQIK NGEHKGRIVV PVYYTNEKGK QSSAVIYSDD SGKNWTIGES PNDNRKLENG KIINSKTLSD DAP QLTECQ VVEMPNGQLK LFMRNLSGYL NIATSFDGGA TWDETVEKDT NVLEPYCQLS VINYSQKVDG KDAVIFSNPN ARSR SNGTV RIGLINQVGT YENGEPKYEF DWKYNKLVKP GYYAYSCLTE LSNGNIGLLY EGTPSEEMSY IEMNLKYLES GANKL ATGA GNTSREAEAL GEGNGPPRDV RNEELAKLEI AVLAVTFAVA VLGNSSVLLA LHRTPRKTSR MHLFIRHLSL ADLAVA FFQ VLPQMCWKIT YRFRGPDWLC RVVKHLQVFG MFASAYMLVV MTADRYIAVC HPLKTLQQPA RRSRLMIAAA WVLSFVL ST PQYFVFSMIE VNNVTKARDC WATFIQPWGS RAYVTWMTGG IFVAPVVILG TCYGFICYNI WCNVRGKTAS RQSKGAEQ A GVAFQKGFLL APCVSSVKSI SRAKIRTVKM TFVIVTAYIV CWAPFFIIQM WSVWDPMSVW TESENPTITI TALLGSLNS CCNPWIYMFF SGHLLQDCVQ SFPCCQNMKE KFNKEDTLEV LFQGPHHHHH HHHHH

UniProtKB: exo-alpha-sialidase, Vasopressin V1a receptor

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Macromolecule #2: Arg-vasopressin

MacromoleculeName: Arg-vasopressin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.086248 KDa
SequenceString:
CYFQNCP(DAR)G(NH2)

UniProtKB: Vasopressin-neurophysin 2-copeptin

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Macromolecule #3: Guanine nucleotide-binding protein G(q) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(q) subunit alpha-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.084832 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSTVSAEDK AAAERSKMID KNLREDGEKA RRTLRLLLLG ADNSGKSTIV KQMRILHGGS GGSGGTSGIF ETKFQVDKVN FHMFDVGGQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA ...String:
MGSTVSAEDK AAAERSKMID KNLREDGEKA RRTLRLLLLG ADNSGKSTIV KQMRILHGGS GGSGGTSGIF ETKFQVDKVN FHMFDVGGQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA RYTTPEDATP EPGEDPRVTR AKYFIRKEFV DISTASGDGR HICYPHFTCA VDTENARRIF NDCKDIILQM NL REYNLV

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.055867 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI ...String:
MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DI NAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDALKADRAG VLA GHDNRV SCLGVTDDGM AVATGSWDSF LKIWNGSSGG GGSGGGGSSG VSGWRLFKKI S

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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.057271 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAMQVQLQES GGGLVQPGGS LRLSCAASGF TFSNYKMNWV RQAPGKGLEW VSDISQSGAS ISYTGSVKG RFTISRDNAK NTLYLQMNSL KPEDTAVYYC ARCPAPFTRD CFDVTSTTYA YRGQGTQVTV SSHHHHHH

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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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 310743
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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