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- EMDB-15024: Structure of the human sodium/bile acid cotransporter (NTCP) in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-15024
TitleStructure of the human sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody
Map dataNanodisc-reconstituted human NTCP in a complex with NTCP_Fab12 and a nanobody in the presence of substrate.
Sample
  • Complex: sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody
    • Protein or peptide: Sodium/bile acid cotransporter
    • Protein or peptide: heavy chain of Fab
    • Protein or peptide: light chain of Fab
    • Protein or peptide: NanobodySingle-domain antibody
  • Ligand: CHOLESTEROL
  • Ligand: GLYCOCHENODEOXYCHOLIC ACID
  • Ligand: SODIUM IONSodium
  • Ligand: water
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 / response to nutrient levels / response to organic cyclic compound / response to estrogen / cellular response to xenobiotic stimulus / virus receptor activity ...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 / 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 / plasma membrane
Similarity search - Function
Bile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily
Similarity search - Domain/homology
Hepatic sodium/bile acid cotransporter
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsLiu H / Irobalieva RN / Bang-Sorensen R / Nosol K / Mukherjee S / Agrawal P / Stieger B / Kossiakoff AA / Locher KP
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Cell Res / Year: 2022
Title: Structure of human NTCP reveals the basis of recognition and sodium-driven transport of bile salts into the liver.
Authors: Hongtao Liu / Rossitza N Irobalieva / Rose Bang-Sørensen / Kamil Nosol / Somnath Mukherjee / Parth Agrawal / Bruno Stieger / Anthony A Kossiakoff / Kaspar P Locher /
History
DepositionMay 24, 2022-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15024.png

Downloads & links

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Map

FileDownload / File: emd_15024.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNanodisc-reconstituted human NTCP in a complex with NTCP_Fab12 and a nanobody in the presence of substrate.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.024857622 - 0.04221448
Average (Standard dev.)3.0879707e-07 (±0.0010721614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_15024_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15024_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody

EntireName: sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody
Components
  • Complex: sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody
    • Protein or peptide: Sodium/bile acid cotransporter
    • Protein or peptide: heavy chain of Fab
    • Protein or peptide: light chain of Fab
    • Protein or peptide: NanobodySingle-domain antibody
  • Ligand: CHOLESTEROL
  • Ligand: GLYCOCHENODEOXYCHOLIC ACID
  • Ligand: SODIUM IONSodium
  • Ligand: water

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Supramolecule #1: sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody

SupramoleculeName: sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: Sodium/bile acid cotransporter

MacromoleculeName: Sodium/bile acid cotransporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.149949 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: heavy chain of Fab

MacromoleculeName: heavy chain of Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.582521 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYSSIHWV RQAPGKGLEW VASISSSYGY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYMKQQSQM WYQRYWGFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYSSIHWV RQAPGKGLEW VASISSSYGY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYMKQQSQM WYQRYWGFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT

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Macromolecule #3: light chain of Fab

MacromoleculeName: light chain of Fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.417971 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYWSPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYWSPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.118386 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VQLQESGGGL VQPGGSLRLS CAASGRTISR YAMSWFRQAP GKEREFVAVA RRSGDGAFYA DSVQGRFTVS RDDAKNTVYL QMNSLKPED TAVYYCAIDS DTFYSGSYDY WGQGTQVTVS S

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #6: GLYCOCHENODEOXYCHOLIC ACID

MacromoleculeName: GLYCOCHENODEOXYCHOLIC ACID / type: ligand / ID: 6 / Number of copies: 2 / Formula: CHO
Molecular weightTheoretical: 449.623 Da
Chemical component information

ChemComp-CHO:
GLYCOCHENODEOXYCHOLIC ACID / detergent*YM / Glycochenodeoxycholic acid

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Macromolecule #7: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 7 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 13208 / Average exposure time: 2.0 sec. / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 161093
FSC plot (resolution estimation)

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