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

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Basic information

Entry
Database: PDB / ID: 8xcd
TitleMacaca fascicularis NTCP in complex with YN69083 Fab
Components
  • Solute carrier family 10 member a1
  • YN69083 Fab Heavy chain
  • YN69083 Fab Light chain
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / transporter / 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 / TAUROCHOLIC ACID / Solute carrier family 10 member a1
Function and homology information
Biological speciesMacaca fascicularis (crab-eating macaque)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsPark, J.H. / Ishimoto, N. / Park, S.Y.
Funding support1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Solute carrier family 10 member a1
H: YN69083 Fab Heavy chain
L: YN69083 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1355
Polymers89,1043
Non-polymers1,0312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Solute carrier family 10 member a1


Mass: 38303.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: Slc10a1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G7PAR4
#2: Antibody YN69083 Fab Heavy chain


Mass: 27418.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody YN69083 Fab Light chain


Mass: 23382.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Chemical ChemComp-TCH / TAUROCHOLIC ACID


Mass: 515.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H45NO7S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Macaca fascicularis NTCP in complex with YN69083 Fab / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.089 MDa / Experimental value: YES
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 4.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 74.057 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3283804
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 226937 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 7FCI

7fci


Accession code: 7FCI / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055764
ELECTRON MICROSCOPYf_angle_d0.6427854
ELECTRON MICROSCOPYf_dihedral_angle_d6.451789
ELECTRON MICROSCOPYf_chiral_restr0.042922
ELECTRON MICROSCOPYf_plane_restr0.005959

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