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Yorodumi- EMDB-26590: CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26590 | |||||||||
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Title | CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab | |||||||||
Map data | Focused refinement map on receptor-nanobody | |||||||||
Sample |
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Keywords | Antagonist / Complex / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information gastric acid secretion / Histamine receptors / histamine receptor activity / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of vasoconstriction / G alpha (s) signalling events / chemical synaptic transmission / immune response ...gastric acid secretion / Histamine receptors / histamine receptor activity / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of vasoconstriction / G alpha (s) signalling events / chemical synaptic transmission / immune response / dendrite / synapse / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Robertson MJ / Skiniotis G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Structure determination of inactive-state GPCRs with a universal nanobody. Authors: Michael J Robertson / Makaía M Papasergi-Scott / Feng He / Alpay B Seven / Justin G Meyerowitz / Ouliana Panova / Maria Claudia Peroto / Tao Che / Georgios Skiniotis / Abstract: Cryogenic electron microscopy (cryo-EM) has widened the field of structure-based drug discovery by allowing for routine determination of membrane protein structures previously intractable. Despite ...Cryogenic electron microscopy (cryo-EM) has widened the field of structure-based drug discovery by allowing for routine determination of membrane protein structures previously intractable. Despite representing one of the largest classes of therapeutic targets, most inactive-state G protein-coupled receptors (GPCRs) have remained inaccessible for cryo-EM because their small size and membrane-embedded nature impedes projection alignment for high-resolution map reconstructions. Here we demonstrate that the same single-chain camelid antibody (nanobody) recognizing a grafted intracellular loop can be used to obtain cryo-EM structures of inactive-state GPCRs at resolutions comparable or better than those obtained by X-ray crystallography. Using this approach, we obtained structures of neurotensin 1 receptor bound to antagonist SR48692, μ-opioid receptor bound to alvimopan, apo somatostatin receptor 2 and histamine receptor 2 bound to famotidine. We expect this rapid, straightforward approach to facilitate the broad exploration of GPCR inactive states without the need for extensive engineering and crystallization. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26590.map.gz | 194.9 MB | EMDB map data format | |
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Header (meta data) | emd-26590-v30.xml emd-26590.xml | 21 KB 21 KB | Display Display | EMDB header |
Images | emd_26590.png | 87.4 KB | ||
Filedesc metadata | emd-26590.cif.gz | 6.1 KB | ||
Others | emd_26590_additional_1.map.gz emd_26590_half_map_1.map.gz emd_26590_half_map_2.map.gz | 197.7 MB 194.1 MB 194.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26590 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26590 | HTTPS FTP |
-Validation report
Summary document | emd_26590_validation.pdf.gz | 827 KB | Display | EMDB validaton report |
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Full document | emd_26590_full_validation.pdf.gz | 826.6 KB | Display | |
Data in XML | emd_26590_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | emd_26590_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26590 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26590 | HTTPS FTP |
-Related structure data
Related structure data | 7ul3MC 7ul2C 7ul4C 7ul5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26590.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Focused refinement map on receptor-nanobody | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8677 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_26590_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26590_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26590_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of H2R, Nb6M, and NabFab
Entire | Name: Complex of H2R, Nb6M, and NabFab |
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Components |
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-Supramolecule #1: Complex of H2R, Nb6M, and NabFab
Supramolecule | Name: Complex of H2R, Nb6M, and NabFab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: H2R
Supramolecule | Name: H2R / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Nb6M
Supramolecule | Name: Nb6M / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: Lama glama (llama) |
-Supramolecule #4: NabFab
Supramolecule | Name: NabFab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: Histamine H2 receptor
Macromolecule | Name: Histamine H2 receptor / 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: 44.770184 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: DYKDDDDAMG QPGNGSAFLL APNRSHAPDH DVENLYFQGM APNGTASSFC LDSTACKITI TVVLAVLILI TVAGNVVVCL AVGLNRRLR NLTNCFIVSL AITDLLLGLL VLPFSAIYQL SCKWSFGKVF CNIYTSLDVM LCTASILNLF MISLDRYCAV M DPLRYPVL ...String: DYKDDDDAMG QPGNGSAFLL APNRSHAPDH DVENLYFQGM APNGTASSFC LDSTACKITI TVVLAVLILI TVAGNVVVCL AVGLNRRLR NLTNCFIVSL AITDLLLGLL VLPFSAIYQL SCKWSFGKVF CNIYTSLDVM LCTASILNLF MISLDRYCAV M DPLRYPVL VTPVRVAISL VLIWVISITL SFLSIHLGWN SRNETSKGNH TTSKCKVQVN EVYGLVDGLV TFYLPLLIMC VC YTLMILR LKSVRLLSGS REKDRNLRRI TRLVLVVVAV FVICWFPYFT AFVYRGLRGD DAINEVLEAI VLWLGYANSA LNP ILYAAL NRDFRTGYQQ LFCCRLANRN SHKTSLRSNA SQLSRTQSRE PRQQEEKPLK LQVWSGTEVT APQGATDRLE VLFQ UniProtKB: Histamine H2 receptor, Kappa-type opioid receptor, Histamine H2 receptor |
-Macromolecule #2: Nanobody 6M
Macromolecule | Name: Nanobody 6M / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.418919 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QRQLVESGGG LVQPGGSLRL SCAASGTIFR LYDMGWFRQA PGKEREGVAS ITSGGSTKYA DSVKGRFTIS RDNAKNTVYL QMNSLEPED TAVYYCNAEY RTGIWEELLD GWGKGTPVTV SSHHHHHHEP EA |
-Macromolecule #3: NabFab HC
Macromolecule | Name: NabFab HC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 25.684463 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NFSYYSIHWV RQAPGKGLEW VAYISSSSSY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARGYQYWQYH ASWYWNGGLD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NFSYYSIHWV RQAPGKGLEW VAYISSSSSY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARGYQYWQYH ASWYWNGGLD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCDKTH T |
-Macromolecule #4: NabFab LC
Macromolecule | Name: NabFab LC / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 23.258783 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #5: famotidine
Macromolecule | Name: famotidine / type: ligand / ID: 5 / Number of copies: 1 / Formula: FO9 |
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Molecular weight | Theoretical: 339.461 Da |
Chemical component information | ChemComp-FO9: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.58 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 365068 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: ANGULAR RECONSTITUTION |