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- EMDB-33557: Cryo-EM structure of apo-state MrgD-Gi complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33557
TitleCryo-EM structure of apo-state MrgD-Gi complex
Map datapost-process map
Sample
  • Complex: MrgD-Gi complex with the scFv16
    • Complex: G(i) subunit alpha-1,Mas-related G-protein coupled receptor member D
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
    • Complex: subunit beta-1,subunit gamma-2
      • 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
    • Complex: scFV16
      • Protein or peptide: scFV16
  • Ligand: PALMITIC ACID
Function / homology
Function and homology information


Activation of the phototransduction cascade / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through BTK / Glucagon-type ligand receptors / G alpha (z) signalling events ...Activation of the phototransduction cascade / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through BTK / Glucagon-type ligand receptors / G alpha (z) signalling events / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / G alpha (s) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Activation of G protein gated Potassium channels / Ca2+ pathway / G alpha (q) signalling events / Extra-nuclear estrogen signaling / G alpha (12/13) signalling events / G alpha (i) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / phototransduction, visible light / ADP signalling through P2Y purinoceptor 1 / alkylglycerophosphoethanolamine phosphodiesterase activity / photoreceptor outer segment membrane / spectrin binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / cell cortex region / G protein-coupled serotonin receptor binding / regulation of cAMP-mediated signaling / photoreceptor outer segment / cellular response to forskolin / regulation of mitotic spindle organization / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / G-protein beta/gamma-subunit complex binding / cardiac muscle cell apoptotic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / sensory perception of taste / Regulation of insulin secretion / photoreceptor inner segment / G-protein beta-subunit binding / GPER1 signaling / heterotrimeric G-protein complex / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / signaling receptor complex adaptor activity / response to peptide hormone / ADORA2B mediated anti-inflammatory cytokines production / phospholipase C-activating G protein-coupled receptor signaling pathway / GTPase binding / G protein-coupled receptor binding / retina development in camera-type eye / G alpha (s) signalling events / GDP binding / G alpha (i) signalling events / fibroblast proliferation / cell body / cell cortex / midbody / cellular response to hypoxia / cell population proliferation / myelin sheath / positive regulation of cytosolic calcium ion concentration / Extra-nuclear estrogen signaling / lysosomal membrane / electron transfer activity / periplasmic space / G protein-coupled receptor signaling pathway / cell cycle / GTPase activity / iron ion binding / cell division / centrosome / dendrite / protein-containing complex binding / GTP binding / heme binding / magnesium ion binding / extracellular space / extracellular exosome / membrane => GO:0016020 / plasma membrane / nucleus / cytoplasm
Similarity search - Function
Mas-related G protein-coupled receptor D / Mas-related G protein-coupled receptor family / Cytochrome b562 / Cytochrome b562 / G-protein alpha subunit, group I / Cytochrome c/b562 / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit / G protein alpha subunit, helical insertion ...Mas-related G protein-coupled receptor D / Mas-related G protein-coupled receptor family / Cytochrome b562 / Cytochrome b562 / G-protein alpha subunit, group I / Cytochrome c/b562 / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-protein gamma subunit domain profile. / G-protein, gamma subunit / G-protein gamma-like domain superfamily / G protein gamma subunit-like motifs / GGL domain / G-protein gamma-like domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 7 transmembrane receptor (rhodopsin family) / G-protein coupled receptors family 1 profile. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / 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
Soluble cytochrome b562 / 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 / Mas-related G-protein coupled receptor member D
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / synthetic construct (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSuzuki S / Iida M / Kawamoto A / Oshima A
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H03165 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101074 Japan
CitationJournal: To Be Published
Title: Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein
Authors: Suzuki S / Iida M / Hiroaki Y / Tanaka K / Kawamoto A / Kato T / Oshima A
History
DepositionJun 6, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateJul 20, 2022-
Current statusJul 20, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_33557.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-process map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 320 pix.
= 216. Å
0.68 Å/pix.
x 320 pix.
= 216. Å
0.68 Å/pix.
x 320 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.550976 - 4.03655
Average (Standard dev.)-0.00090219476 (±0.08722593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33557_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map 1

Fileemd_33557_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half map 2

Fileemd_33557_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : MrgD-Gi complex with the scFv16

EntireName: MrgD-Gi complex with the scFv16
Components
  • Complex: MrgD-Gi complex with the scFv16
    • Complex: G(i) subunit alpha-1,Mas-related G-protein coupled receptor member D
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
    • Complex: subunit beta-1,subunit gamma-2
      • 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
    • Complex: scFV16
      • Protein or peptide: scFV16
  • Ligand: PALMITIC ACID

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Supramolecule #1: MrgD-Gi complex with the scFv16

SupramoleculeName: MrgD-Gi complex with the scFv16 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: G(i) subunit alpha-1,Mas-related G-protein coupled receptor member D

SupramoleculeName: G(i) subunit alpha-1,Mas-related G-protein coupled receptor member D
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: subunit beta-1,subunit gamma-2

SupramoleculeName: subunit beta-1,subunit gamma-2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: synthetic construct (unknown)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #4: scFV16

SupramoleculeName: scFV16 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5

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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: 40.446047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV AAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY QEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 39.46107 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHE NLYFQGSSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSA SQDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT G YLSCCRFL ...String:
MHHHHHHHHE NLYFQGSSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSA SQDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT G YLSCCRFL DDNQIVTSSG DTTCALWDIE TGQQTTTFTG HTGDVMSLSL APDTRLFVSG ACDASAKLWD VREGMCRQTF TG HESDINA ICFFPNGNAF ATGSDDATCR LFDLRADQEL MTYSHDNIIC GITSVSFSKS GRLLLAGYDD FNCNVWDALK ADR AGVLAG HDNRVSCLGV TDDGMAVATG SWDSFLKIWN

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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Macromolecule #4: Soluble cytochrome b562,Mas-related G-protein coupled receptor me...

MacromoleculeName: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.141285 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LNSSGTVESA LNYSRGSTVH TAYLVLSSLA M FTCLCGMA ...String:
MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LNSSGTVESA LNYSRGSTVH TAYLVLSSLA M FTCLCGMA GNSMVIWLLG FRMHRNPFCI YILNLAAADL LFLFSMASTL SLETQPLVNT TDKVHELMKR LMYFAYTVGL SL LTAISTQ RCLSVLFPIW FKCHRPRHLS AWVCGLLWTL CLLMNGLTSS FCSKFLKFNE DRCFRVDMVQ AALIMGVLTP VMT LSSLTL FVWVRRSSQQ WRRQPTRLFV VVLASVLVFL ICSLPLSIYW FVLYWLSLPP EMQVLCFSLS RLSSSVSSSA NPVI YFLVG SRRSHRLPTR SLGTVLQQAL REEPELEGGE TPTVGTNEMG A

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Macromolecule #5: scFV16

MacromoleculeName: scFV16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (unknown)
Molecular weightTheoretical: 31.739434 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LLVNQSHQGF NKEHTSKMVS AIVLYVLLAA AAHSAFADVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSSG G GGSGGGGS ...String:
LLVNQSHQGF NKEHTSKMVS AIVLYVLLAA AAHSAFADVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSSG G GGSGGGGS GGGGSDIVMT QATSSVPVTP GESVSISCRS SKSLLHSNGN TYLYWFLQRP GQSPQLLIYR MSNLASGVPD RF SGSGSGT AFTLTISRLE AEDVGVYYCM QHLEYPLTFG AGTKLELKAA AHHHHHHHH

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 3 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

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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

Concentration10 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 3 seconds blot force 5.

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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 / Cs: 0.01 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm
Specialist opticsSpherical aberration corrector: The Microscope implicated Cs corrector.
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 349331
FSC plot (resolution estimation)

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