[English] 日本語
![](img/lk-miru.gif)
- EMDB-26590: CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab | |||||||||
![]() | Focused refinement map on receptor-nanobody | |||||||||
![]() |
| |||||||||
Function / homology | ![]() gastric acid secretion / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Robertson MJ / Skiniotis G | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 194.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
Images | ![]() | 87.4 KB | ||
Others | ![]() ![]() ![]() | 197.7 MB 194.1 MB 194.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ul3MC ![]() 7ul2C ![]() 7ul4C ![]() 7ul5C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Focused refinement map on receptor-nanobody | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8677 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: #1
File | emd_26590_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_26590_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_26590_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Complex of H2R, Nb6M, and NabFab
Entire | Name: Complex of H2R, Nb6M, and NabFab |
---|---|
Components |
|
-Supramolecule #1: Complex of H2R, Nb6M, and NabFab
Supramolecule | Name: Complex of H2R, Nb6M, and NabFab / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: H2R
Supramolecule | Name: H2R / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Nb6M
Supramolecule | Name: Nb6M / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #4 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
-Supramolecule #4: NabFab
Supramolecule | Name: NabFab / type: complex / ID: 4 / Chimera: Yes / Parent: 1 / Macromolecule list: #3-#4 |
---|---|
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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 44.770184 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 |
-Macromolecule #2: Nanobody 6M
Macromolecule | Name: Nanobody 6M / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.418919 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 25.684463 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 23.258783 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 |
---|---|
Molecular weight | Theoretical: 339.461 Da |
Chemical component information | ![]() ChemComp-FO9: |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.58 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Initial angle assignment | Type: OTHER |
---|---|
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 365068 |