+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19440 | |||||||||||||||
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Title | Cryo-EM structure of human NTCP-Bulevirtide complex | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Hepatitis B/D virus receptor / bile salt transporter / drugs / inhibitor / TRANSPORT PROTEIN | |||||||||||||||
Function / homology | Function and homology information bile acid:sodium symporter activity / regulation of bile acid secretion / bile acid and bile salt transport / bile acid signaling pathway / Recycling of bile acids and salts / viral process / response to nutrient levels / response to organic cyclic compound / response to estrogen / cellular response to xenobiotic stimulus ...bile acid:sodium symporter activity / regulation of bile acid secretion / bile acid and bile salt transport / bile acid signaling pathway / Recycling of bile acids and salts / viral process / response to nutrient levels / response to organic cyclic compound / response to estrogen / cellular response to xenobiotic stimulus / virus receptor activity / basolateral plasma membrane / response to ethanol / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) / hepatitis B virus genotype C | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||||||||
Authors | Liu H / Zakrzewicz D / Nosol K / Irobalieva RN / Mukherjee S / Bang-Soerensen R / Goldmann N / Kunz S / Rossi L / Kossiakoff AA ...Liu H / Zakrzewicz D / Nosol K / Irobalieva RN / Mukherjee S / Bang-Soerensen R / Goldmann N / Kunz S / Rossi L / Kossiakoff AA / Urban S / Glebe D / Geyer J / Locher KP | |||||||||||||||
Funding support | Switzerland, Germany, United States, 4 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human NTCP-Bulevirtide complex Authors: Liu H / Zakrzewicz D / Nosol K / Irobalieva RN / Mukherjee S / Bang-Sorensen R / Goldmann N / Kunz S / Rossi L / Kossiakoff AA / Urban S / Glebe D / Geyer J / Locher KP | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19440.map.gz | 203.6 MB | EMDB map data format | |
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Header (meta data) | emd-19440-v30.xml emd-19440.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
Images | emd_19440.png | 73.7 KB | ||
Masks | emd_19440_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-19440.cif.gz | 6.4 KB | ||
Others | emd_19440_half_map_1.map.gz emd_19440_half_map_2.map.gz | 200.1 MB 200.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19440 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19440 | HTTPS FTP |
-Validation report
Summary document | emd_19440_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_19440_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_19440_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_19440_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19440 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19440 | HTTPS FTP |
-Related structure data
Related structure data | 8rqfMC 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_19440.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19440_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19440_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19440_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of Bulevirtide-bound human NTCP in complex with Fab and...
Entire | Name: Structure of Bulevirtide-bound human NTCP in complex with Fab and nanobody |
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Components |
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-Supramolecule #1: Structure of Bulevirtide-bound human NTCP in complex with Fab and...
Supramolecule | Name: Structure of Bulevirtide-bound human NTCP in complex with Fab and nanobody type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: Sodium/bile acid cotransporter
Macromolecule | Name: Sodium/bile acid cotransporter / 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: 38.149949 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEAHNASAPF NFTLPPNFGK RPTDLALSVI LVFMLFFIML SLGCTMEFSK IKAHLWKPKG LAIALVAQYG IMPLTAFVLG KVFRLKNIE ALAILVCGCS PGGNLSNVFS LAMKGDMNLS IVMTTCSTFC ALGMMPLLLY IYSRGIYDGD LKDKVPYKGI V ISLVLVLI ...String: MEAHNASAPF NFTLPPNFGK RPTDLALSVI LVFMLFFIML SLGCTMEFSK IKAHLWKPKG LAIALVAQYG IMPLTAFVLG KVFRLKNIE ALAILVCGCS PGGNLSNVFS LAMKGDMNLS IVMTTCSTFC ALGMMPLLLY IYSRGIYDGD LKDKVPYKGI V ISLVLVLI PCTIGIVLKS KRPQYMRYVI KGGMIIILLC SVAVTVLSAI NVGKSIMFAM TPLLIATSSL MPFIGFLLGY VL SALFCLN GRCRRTVSME TGCQNVQLCS TILNVAFPPE VIGPLFFFPL LYMIFQLGEG LLLIAIFWCY EKFKTPKDKT KMI YTAATT EETIPGALGN GTYKGEDCSP CTA UniProtKB: Hepatic sodium/bile acid cotransporter |
-Macromolecule #2: Heavy chain of Fab3
Macromolecule | Name: Heavy chain of Fab3 / 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: 25.197955 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSSYIHWV RQAPGKGLEW VASISPYYSY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYQYDYYYS YYAGLDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSSYIHWV RQAPGKGLEW VASISPYYSY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYQYDYYYS YYAGLDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDKTHT |
-Macromolecule #3: Light chain of Fab3
Macromolecule | Name: Light chain of Fab3 / 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: 23.481094 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYRYSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYRYSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #4: Fab-specific nanobody
Macromolecule | Name: Fab-specific nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 13.118386 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: VQLQESGGGL VQPGGSLRLS CAASGRTISR YAMSWFRQAP GKEREFVAVA RRSGDGAFYA DSVQGRFTVS RDDAKNTVYL QMNSLKPED TAVYYCAIDS DTFYSGSYDY WGQGTQVTVS S |
-Macromolecule #5: Polymerase
Macromolecule | Name: Polymerase / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: hepatitis B virus genotype C |
Molecular weight | Theoretical: 5.136473 KDa |
Sequence | String: TNLSVPNPLG FFPDHQLDPA FGANSNNPDW DFNPNKDHWP EANKVG UniProtKB: Polymerase |
-Macromolecule #6: N-tetradecanoylglycine
Macromolecule | Name: N-tetradecanoylglycine / type: ligand / ID: 6 / Number of copies: 1 / Formula: BJU |
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Molecular weight | Theoretical: 285.422 Da |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 1 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128700 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |