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- EMDB-38240: Macaca fascicularis NTCP in complex with YN69083 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-38240
TitleMacaca fascicularis NTCP in complex with YN69083 Fab
Map datasharpening map
Sample
  • Complex: Macaca fascicularis NTCP in complex with YN69083 Fab
    • Protein or peptide: Solute carrier family 10 member a1
    • Protein or peptide: YN69083 Fab Heavy chain
    • Protein or peptide: YN69083 Fab Light chain
  • Ligand: TAUROCHOLIC ACID
Keywordstransporter / transport protein-immune system complex
Function / homologybile acid:sodium symporter activity / Bile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / membrane / Solute carrier family 10 member a1
Function and homology information
Biological speciesMacaca fascicularis (crab-eating macaque) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsPark JH / Ishimoto N / Park SY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for hepatitis B virus restriction by a viral receptor homologue.
Authors: Kaho Shionoya / Jae-Hyun Park / Toru Ekimoto / Junko S Takeuchi / Junki Mifune / Takeshi Morita / Naito Ishimoto / Haruka Umezawa / Kenichiro Yamamoto / Chisa Kobayashi / Atsuto Kusunoki / ...Authors: Kaho Shionoya / Jae-Hyun Park / Toru Ekimoto / Junko S Takeuchi / Junki Mifune / Takeshi Morita / Naito Ishimoto / Haruka Umezawa / Kenichiro Yamamoto / Chisa Kobayashi / Atsuto Kusunoki / Norimichi Nomura / So Iwata / Masamichi Muramatsu / Jeremy R H Tame / Mitsunori Ikeguchi / Sam-Yong Park / Koichi Watashi /
Abstract: Macaque restricts hepatitis B virus (HBV) infection because its receptor homologue, NTCP (mNTCP), cannot bind preS1 on viral surface. To reveal how mNTCP loses the viral receptor function, we here ...Macaque restricts hepatitis B virus (HBV) infection because its receptor homologue, NTCP (mNTCP), cannot bind preS1 on viral surface. To reveal how mNTCP loses the viral receptor function, we here solve the cryo-electron microscopy structure of mNTCP. Superposing on the human NTCP (hNTCP)-preS1 complex structure shows that Arg158 of mNTCP causes steric clash to prevent preS1 from embedding onto the bile acid tunnel of NTCP. Cell-based mutation analysis confirms that only Gly158 permitted preS1 binding, in contrast to robust bile acid transport among mutations. As the second determinant, Asn86 on the extracellular surface of mNTCP shows less capacity to restrain preS1 from dynamic fluctuation than Lys86 of hNTCP, resulting in unstable preS1 binding. Additionally, presence of long-chain conjugated-bile acids in the tunnel induces steric hindrance with preS1 through their tailed-chain. This study presents structural basis in which multiple sites in mNTCP constitute a molecular barrier to strictly restrict HBV.
History
DepositionDec 8, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38240.png

Downloads & links

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Map

FileDownload / File: emd_38240.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpening map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.2991246 - 1.7428995
Average (Standard dev.)0.0018034346 (±0.035460163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38240_msk_1.map
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Additional map: unsharpened map

Fileemd_38240_additional_1.map
Annotationunsharpened map
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Half map: half map A

Fileemd_38240_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_38240_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : Macaca fascicularis NTCP in complex with YN69083 Fab

EntireName: Macaca fascicularis NTCP in complex with YN69083 Fab
Components
  • Complex: Macaca fascicularis NTCP in complex with YN69083 Fab
    • Protein or peptide: Solute carrier family 10 member a1
    • Protein or peptide: YN69083 Fab Heavy chain
    • Protein or peptide: YN69083 Fab Light chain
  • Ligand: TAUROCHOLIC ACID

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Supramolecule #1: Macaca fascicularis NTCP in complex with YN69083 Fab

SupramoleculeName: Macaca fascicularis NTCP in complex with YN69083 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 89 KDa

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Macromolecule #1: Solute carrier family 10 member a1

MacromoleculeName: Solute carrier family 10 member a1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 38.303047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMEAHNASA PFNFTLPPNF GKRPTDLALS IILVFMLFFV MLSLGCTMEF SKIKAHLWKP KGLAIALVAQ YGIMPLTAFV LGKVFQLNN IEALAILVCG CSPGGNLSNV FSLAMKGDMN LSIVMTTCST FCALGMMPLL LYLYTRGIYD GDLKDKVPYG R IILSLVPV ...String:
GPMEAHNASA PFNFTLPPNF GKRPTDLALS IILVFMLFFV MLSLGCTMEF SKIKAHLWKP KGLAIALVAQ YGIMPLTAFV LGKVFQLNN IEALAILVCG CSPGGNLSNV FSLAMKGDMN LSIVMTTCST FCALGMMPLL LYLYTRGIYD GDLKDKVPYG R IILSLVPV LIPCTIGIVL KSKRPQYMRY VIKGGMIIIL LCSVAVTVLS AINVGKSIMF AMTPLLIATS SLMPFIGFLL GY VLSALFC LNGRCRRTVS METGCQNVQL CSTILNVAFP PEVIGPLFFF PLLYMIFQLG EGLLLIAMFR CYEKFKTPKD KTK MIYTAA TTEETIPAAL GNGTYKGEDC SPCTA

UniProtKB: Solute carrier family 10 member a1

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Macromolecule #2: YN69083 Fab Heavy chain

MacromoleculeName: YN69083 Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.418123 KDa
SequenceString: EVQLQQPGAE LVKPGASVKL SCKTSGYTFT NYWMKWVKQR PGQGLEWIGE INPSNGGTNY NGKFKSKASL TVDKSSSTAY MQLSSLTSE DSAVYYCTIL VYDAYYVFAM DYWGLGTSVT VSSAKTTPPS VYPLAPGSAA QTNSMVTLGC LVKGYFPEPV T VTWNSGSL ...String:
EVQLQQPGAE LVKPGASVKL SCKTSGYTFT NYWMKWVKQR PGQGLEWIGE INPSNGGTNY NGKFKSKASL TVDKSSSTAY MQLSSLTSE DSAVYYCTIL VYDAYYVFAM DYWGLGTSVT VSSAKTTPPS VYPLAPGSAA QTNSMVTLGC LVKGYFPEPV T VTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SETVTCNVAH PASSTKVDKK IVPRDCGCKP CICTVPEVSS VF IFPPKPK DVLTITLT

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Macromolecule #3: YN69083 Fab Light chain

MacromoleculeName: YN69083 Fab Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.3829 KDa
SequenceString: DIVMTQSPAI MSASPGQKVT ITCSASSSVN YMHWYQQKLG SSPKLWIYDT SKLALGVPAR FSGSGSGTSY SLTISSMEAE DAASYFCHQ WSSYPRTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
DIVMTQSPAI MSASPGQKVT ITCSASSSVN YMHWYQQKLG SSPKLWIYDT SKLALGVPAR FSGSGSGTSY SLTISSMEAE DAASYFCHQ WSSYPRTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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Macromolecule #4: TAUROCHOLIC ACID

MacromoleculeName: TAUROCHOLIC ACID / type: ligand / ID: 4 / Number of copies: 2 / Formula: TCH
Molecular weightTheoretical: 515.703 Da
Chemical component information

ChemComp-TCH:
TAUROCHOLIC ACID

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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

Concentration4.8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 74.057 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3283804
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 226937
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7fci


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-8xcd:
Macaca fascicularis NTCP in complex with YN69083 Fab

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