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Yorodumi- EMDB-63326: Cryo-EM structure of the histamine H1 receptor-Gi protein complex -
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Open data
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Basic information
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| Title | Cryo-EM structure of the histamine H1 receptor-Gi protein complex | |||||||||
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Keywords | GPCR / Class A GPCR / Histamine / G protein / Complex / MEMBRANE PROTEIN | |||||||||
| Function / homology | Function and homology informationHistamine receptors / histamine receptor activity / regulation of vascular permeability / cellular response to histamine / 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 ...Histamine receptors / histamine receptor activity / regulation of vascular permeability / cellular response to histamine / 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 / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / 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 / G alpha (12/13) signalling events / Glucagon-type ligand receptors / 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 / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / photoreceptor outer segment membrane / G alpha (s) signalling events / G alpha (q) signalling events / host cell lipid droplet / spectrin binding / G alpha (i) signalling events / symbiont-mediated transformation of host cell / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / symbiont-mediated suppression of host TRAF-mediated signal transduction / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of vasoconstriction / alkylglycerophosphoethanolamine phosphodiesterase activity / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / host cell mitochondrion / photoreceptor outer segment / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cardiac muscle cell apoptotic process / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / photoreceptor inner segment / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / cellular response to forskolin / regulation of mitotic spindle organization / ribonucleoside triphosphate phosphatase activity / bioluminescence / generation of precursor metabolites and energy / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / visual learning / regulation of synaptic plasticity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite / memory / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / GDP binding / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / cellular response to prostaglandin E stimulus Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / ![]() ![]() ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Matsuzaki Y / Sano FK / Oshima HS / Akasaka H / Kobayashi K / Tanaka T / Itoh Y / Shihoya W / Kise Y / Kusakizako T / Nureki O | |||||||||
| Funding support | Japan, 1 items
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Citation | Journal: Commun Biol / Year: 2025Title: Structural insights into ligand recognition and G protein preferences across histamine receptors. Authors: Yuma Matsuzaki / Fumiya K Sano / Hidetaka S Oshima / Hiroaki Akasaka / Kazuhiro Kobayashi / Tatsuki Tanaka / Yuzuru Itoh / Wataru Shihoya / Yoshiaki Kise / Tsukasa Kusakizako / Asuka Inoue / Osamu Nureki / ![]() Abstract: Histamine exerts critical physiological roles by activating four receptor subtypes, each exhibiting a specific G protein preference. Among these, the histamine H receptor (HR) modulates chemotaxis ...Histamine exerts critical physiological roles by activating four receptor subtypes, each exhibiting a specific G protein preference. Among these, the histamine H receptor (HR) modulates chemotaxis and interferon production through G protein activation, suggesting its therapeutic potential. Despite its physiological significance, the mechanisms underlying HR signalling and G protein preference across histamine receptors remain poorly understood. Here, we present the cryo-electron microscopy structure of the HR-G complex, revealing unique mechanisms of histamine recognition and receptor activation. We further solved the structures of the histamine H receptor (HR) bound to the non-canonical G proteins G and G. Through a combination of functional and computational analyses, we identified the intracellular loop 2 as a critical determinant of G protein preference in HR and HR. Collectively, our comprehensive study revealed the structural basis for distinct mechanisms of ligand recognition and receptor activation, offering a profound insight into G protein preference across receptor subtypes. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_63326.map.gz | 1.4 MB | EMDB map data format | |
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| Header (meta data) | emd-63326-v30.xml emd-63326.xml | 25.1 KB 25.1 KB | Display Display | EMDB header |
| Images | emd_63326.png | 110.6 KB | ||
| Masks | emd_63326_msk_1.map | 22.2 MB | Mask map | |
| Filedesc metadata | emd-63326.cif.gz | 7.5 KB | ||
| Others | emd_63326_half_map_1.map.gz emd_63326_half_map_2.map.gz | 20.7 MB 20.7 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-63326 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-63326 | HTTPS FTP |
-Validation report
| Summary document | emd_63326_validation.pdf.gz | 750.1 KB | Display | EMDB validaton report |
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| Full document | emd_63326_full_validation.pdf.gz | 749.7 KB | Display | |
| Data in XML | emd_63326_validation.xml.gz | 10.2 KB | Display | |
| Data in CIF | emd_63326_validation.cif.gz | 12 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-63326 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-63326 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9lrdMC ![]() 9lrbC ![]() 9lrcC ![]() 9lreC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_63326.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.29111 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_63326_msk_1.map | ||||||||||||
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-Half map: #2
| File | emd_63326_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_63326_half_map_2.map | ||||||||||||
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Sample components
-Entire : Histamine H1 receptor-Gi protein complex
| Entire | Name: Histamine H1 receptor-Gi protein complex |
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| Components |
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-Supramolecule #1: Histamine H1 receptor-Gi protein complex
| Supramolecule | Name: Histamine H1 receptor-Gi protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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| Source (natural) | Organism: Homo sapiens (human) |
-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: 40.415031 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: 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 FDVGGQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCA TDTKNVQFVF DAVTDVIIKN NLKDCGLF UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1 |
-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: ![]() |
| Molecular weight | Theoretical: 38.744371 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: 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 LKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-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: ![]() |
| Molecular weight | Theoretical: 7.547685 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFS UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #4: scFv16
| Macromolecule | Name: scFv16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 27.720795 KDa |
| Recombinant expression | Organism: ![]() |
| 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 KAAAASSEDL YFQ |
-Macromolecule #5: Histamine H1 receptor,Genome polyprotein
| Macromolecule | Name: Histamine H1 receptor,Genome polyprotein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 90.333703 KDa |
| Recombinant expression | Organism: Homo sapiens (human) |
| Sequence | String: MKTIIALSYI FCLVFADYKD DDDKEFMSLP NSSCLLEDKM CEGNKTTMAS PQLMPLVVVL STICLVTVGL NLLVLYAVRS ERKLHTVGN LYIVSLSVAD LIVGAVVMPM NILYLLMSKW SLGRPLCLFW LSMDYVASTA SIFSVFILCI DRYRSVQQPL R YLKYRTKT ...String: MKTIIALSYI FCLVFADYKD DDDKEFMSLP NSSCLLEDKM CEGNKTTMAS PQLMPLVVVL STICLVTVGL NLLVLYAVRS ERKLHTVGN LYIVSLSVAD LIVGAVVMPM NILYLLMSKW SLGRPLCLFW LSMDYVASTA SIFSVFILCI DRYRSVQQPL R YLKYRTKT RASATILGAW FLSFLWVIPI LGWNHFMQQT SVRREDKCET DFYDVTWFKV MTAIINFYLP TLLMLWFYAK IY KAVRQHC QHRELINRSL PSFSEIKLRP ENPKGDAKKP GKESPWEVLK RKPKDAGGGS VLKSPSQTPK EMKSPVVFSQ EDD REVDKL YCFPLDIVHM QAAAEGSSRD YVAVNRSHGQ LKTDEQGLNT HGASEISEDQ MLGDSQSFSR TDSDTTTETA PGKG KLRSG SNTGLDYIKF TWKRLRSHSR QYVSGLHMNR ERKAAKQLGF IMAAFILCWI PYFIFFMVIA FCKNCCNEHL HMFTI WLGY INSTLNPLIY PLCNENFKKT FKRILHIRSG GSGGGGSGGS SSGGGSSGGS GGGSGGSGGL EVLFQGPVSK GEELFT GVV PILVELDGDV NGHKFSVSGE GEGDATYGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKQHD FFKSAMP EG YVQERTIFFK DDGNYKTRAE VKFEGDTLVN RIELKGIDFK EDGNILGHKL EYNYNSHNVY IMADKQKNGI KVNFKIRH N IEDGSVQLAD HYQQNTPIGD GPVLLPDNHY LSTQSKLSKD PNEKRDHMVL LEFVTAAGIT LGMDELYKSG LRSHHHHHH HH UniProtKB: Histamine H1 receptor, Genome polyprotein |
-Macromolecule #6: HISTAMINE
| Macromolecule | Name: HISTAMINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: HSM |
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| Molecular weight | Theoretical: 111.145 Da |
| Chemical component information | ![]() ChemComp-HSM: |
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.4 |
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| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10248 / Average electron dose: 48.96 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Japan, 1 items
Citation






























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Processing
FIELD EMISSION GUN

