+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24506 | |||||||||
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Title | Structure of US27-Gi-scFv16 in CL-state | |||||||||
Map data | Full local anisotropic sharpen map (Phenix). | |||||||||
Sample |
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Function / homology | Function and homology information : / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / virus-mediated perturbation of host defense response ...: / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / virus-mediated perturbation of host defense response / virion component / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / Sensory perception of sweet, bitter, and umami (glutamate) taste / response to peptide hormone / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / 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 / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / GDP binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / membrane => GO:0016020 / cell cycle / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / synapse / protein-containing complex binding / GTP binding / nucleolus / host cell plasma membrane / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) / Human betaherpesvirus 5 / Human cytomegalovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Tsutsumi N / Jude KM / Garcia KC | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins Authors: Tsutsumi N / Maeda S / Qu Q / Voegele M / Jude KM / Suomivuori CM / Panova O / Waghray D / Kato HE / Velasco A / Dror RO / Skiniotis G / Kobilka BK / Garcia KC | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24506.map.gz | 96.4 MB | EMDB map data format | |
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Header (meta data) | emd-24506-v30.xml emd-24506.xml | 30.8 KB 30.8 KB | Display Display | EMDB header |
Images | emd_24506.png | 111.9 KB | ||
Others | emd_24506_additional_1.map.gz emd_24506_additional_2.map.gz emd_24506_half_map_1.map.gz emd_24506_half_map_2.map.gz | 53.2 MB 51.9 MB 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24506 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24506 | HTTPS FTP |
-Related structure data
Related structure data | 7rkxMC 7rkfC 7rkmC 7rknC 7rkyC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24506.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full local anisotropic sharpen map (Phenix). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8677 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Full uniform sharpen map used for refinement.
File | emd_24506_additional_1.map | ||||||||||||
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Annotation | Full uniform sharpen map used for refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Full unsharpen map.
File | emd_24506_additional_2.map | ||||||||||||
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Annotation | Full unsharpen map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B.
File | emd_24506_half_map_1.map | ||||||||||||
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Annotation | Half map B. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A.
File | emd_24506_half_map_2.map | ||||||||||||
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Annotation | Half map A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : US27-Gi-scFv16 complex
Entire | Name: US27-Gi-scFv16 complex |
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Components |
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-Supramolecule #1: US27-Gi-scFv16 complex
Supramolecule | Name: US27-Gi-scFv16 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Gi heterotrimer
Supramolecule | Name: Gi heterotrimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) / Location in cell: Membrane |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 90 KDa |
-Supramolecule #3: scFv16
Supramolecule | Name: scFv16 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 30 KDa |
-Supramolecule #4: US27
Supramolecule | Name: US27 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5 |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40 KDa |
-Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-1
Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-1 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40.283836 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 DVGGQRSERK KWIHCFEGVT AIIFCVALSD YDLVLAEDEE MN RMHESMK LFDSICNNKW FTDTSIILFL NKKDLFEEKI KKSPLTICYP EYAGSNTYEE AAAYIQCQFE DLNKRKDTKE IYT HFTCAT DTKNVQFVFD AVTDVIIKNN LKDCGLF |
-Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.728152 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN |
-Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 7.432554 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFC |
-Macromolecule #4: Antibody fragment scFv16
Macromolecule | Name: Antibody fragment scFv16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 27.340482 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Macromolecule #5: G-protein coupled receptor homolog US27
Macromolecule | Name: G-protein coupled receptor homolog US27 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human cytomegalovirus |
Molecular weight | Theoretical: 44.451742 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DYKDDDDMTT STNNQTLTQV SNMTNHTLNS TEIYQLFEYT RLGVWLMCIV GTFLNVLVIT TILYYRRKKK SPSDTYICNL AVADLLIVV GLPFFLEYAK HHPKLSREVV CSGLNACFYI CLFAGVCFLI NLSMDRYCVI VWGVELNRVR NNKRATCWVV I FWILAVLM ...String: DYKDDDDMTT STNNQTLTQV SNMTNHTLNS TEIYQLFEYT RLGVWLMCIV GTFLNVLVIT TILYYRRKKK SPSDTYICNL AVADLLIVV GLPFFLEYAK HHPKLSREVV CSGLNACFYI CLFAGVCFLI NLSMDRYCVI VWGVELNRVR NNKRATCWVV I FWILAVLM GMPHYLMYSH TNNECVGEFA NETSGWFPVF LNTKVNICGY LAPIALMAYT YNRMVRFIIN YVGKWHMQTL HV LLVVVVS FASFWFPFNL ALFLESIRLL AGVYNDTLQN VIIFCLYVGQ FLAYVRACLN PGIYILVGTQ MRKDMWTTLR VFA CCCVKQ EIPYQDIDIE LQKDIQRRAK HTKRTHYDRK NAPMESGEEE FLLSRGAAHH HHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | ||||||||||
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Buffer | pH: 7.2 Component:
Details: additives: 0.01 % w/v fluorinated octyl maltoside or 0.05 % w/v digitonin | ||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 15 mA | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: 3 s blotting before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 57624 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 3 / Number real images: 12233 / Average electron dose: 73.0 e/Å2 Details: The data from the three grids were also used to reconstruct the OCL-state US27-Gi-scFv16 complex (7RKY). |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 12254340 Details: Including non-proteinous features. The actual number of intact complex particles was ~1,159,618. |
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CTF correction | Software - Name: cryoSPARC (ver. 3.1) Details: Final per-particle CTF values were determined by cryoSPARC Local CTF Refinement. |
Startup model | Type of model: OTHER Details: Initial model created by cryoSPARC ab-initio reconstruction. |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final 3D classification | Software - Name: cryoSPARC (ver. 3.1) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.1) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) Details: The resolution estimate was inflated due to the better-defined G protein region compared to the receptor region. Number images used: 268877 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7rkx: |