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Yorodumi- PDB-8p2z: Structure of human SIT1 bound to L-pipecolate (focussed map / ref... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p2z | ||||||
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Title | Structure of human SIT1 bound to L-pipecolate (focussed map / refinement) | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / amino acid transporter / proline / SLC6A20 / ACE2 | ||||||
Function / homology | Function and homology information proline:sodium symporter activity / L-isoleucine transmembrane transporter activity / solute:sodium symporter activity / amino-acid betaine transport / L-isoleucine import across plasma membrane / L-proline import across plasma membrane / Variant SLC6A20 contributes towards hyperglycinuria (HG) and iminoglycinuria (IG) / Variant SLC6A20 contributes towards hyperglycinuria (HG) and iminoglycinuria (IG) / proline import across plasma membrane / L-proline transmembrane transporter activity ...proline:sodium symporter activity / L-isoleucine transmembrane transporter activity / solute:sodium symporter activity / amino-acid betaine transport / L-isoleucine import across plasma membrane / L-proline import across plasma membrane / Variant SLC6A20 contributes towards hyperglycinuria (HG) and iminoglycinuria (IG) / Variant SLC6A20 contributes towards hyperglycinuria (HG) and iminoglycinuria (IG) / proline import across plasma membrane / L-proline transmembrane transporter activity / glycine import across plasma membrane / amino-acid betaine transmembrane transporter activity / glycine transport / amino acid import across plasma membrane / proline transport / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / amino acid transport / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / transport across blood-brain barrier / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / sodium ion transmembrane transport / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / receptor-mediated virion attachment to host cell / symbiont entry into host cell / apical plasma membrane / membrane raft / endoplasmic reticulum lumen / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Li, H.Z. / Pike, A.C.W. / Chi, G. / Hansen, J.S. / Lee, S.G. / Rodstrom, K.E.J. / Bushell, S.R. / Speedman, D. / Evans, A. / Wang, D. ...Li, H.Z. / Pike, A.C.W. / Chi, G. / Hansen, J.S. / Lee, S.G. / Rodstrom, K.E.J. / Bushell, S.R. / Speedman, D. / Evans, A. / Wang, D. / He, D. / Shrestha, L. / Nasrallah, C. / Chalk, R. / Moreira, T. / MacLean, E.M. / Marsden, B. / Bountra, C. / Burgess-Brown, N.A. / Dafforn, T.R. / Carpenter, E.P. / Sauer, D.B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2. Authors: Huanyu Z Li / Ashley C W Pike / Irina Lotsaris / Gamma Chi / Jesper S Hansen / Sarah C Lee / Karin E J Rödström / Simon R Bushell / David Speedman / Adam Evans / Dong Wang / Didi He / ...Authors: Huanyu Z Li / Ashley C W Pike / Irina Lotsaris / Gamma Chi / Jesper S Hansen / Sarah C Lee / Karin E J Rödström / Simon R Bushell / David Speedman / Adam Evans / Dong Wang / Didi He / Leela Shrestha / Chady Nasrallah / Nicola A Burgess-Brown / Robert J Vandenberg / Timothy R Dafforn / Elisabeth P Carpenter / David B Sauer / Abstract: Proline is widely known as the only proteogenic amino acid with a secondary amine. In addition to its crucial role in protein structure, the secondary amino acid modulates neurotransmission and ...Proline is widely known as the only proteogenic amino acid with a secondary amine. In addition to its crucial role in protein structure, the secondary amino acid modulates neurotransmission and regulates the kinetics of signaling proteins. To understand the structural basis of proline import, we solved the structure of the proline transporter SIT1 in complex with the COVID-19 viral receptor ACE2 by cryo-electron microscopy. The structure of pipecolate-bound SIT1 reveals the specific sequence requirements for proline transport in the SLC6 family and how this protein excludes amino acids with extended side chains. By comparing apo and substrate-bound SIT1 states, we also identify the structural changes that link substrate release and opening of the cytoplasmic gate and provide an explanation for how a missense mutation in the transporter causes iminoglycinuria. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p2z.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p2z.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 8p2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/8p2z ftp://data.pdbj.org/pub/pdb/validation_reports/p2/8p2z | HTTPS FTP |
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-Related structure data
Related structure data | 17380MC 8p2wC 8p2xC 8p2yC 8p30C 8p31C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 93425.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ACE2 TMD / Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Details (production host): pHTBV1.1-CT10H-SIII-LIC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9BYF1 | ||||||
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#2: Protein | Mass: 71376.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A20, SIT1, XT3, XTRP3 / Plasmid: pHTBV1.1-CT10H-SIII-LIC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NP91 | ||||||
#3: Sugar | #4: Chemical | ChemComp-YCP / ( | #5: Chemical | ChemComp-CL / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SIT1:ACE2 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.34 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: grid blotted for 4sec after a 20sec wait time |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.77 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13194 Details: Images were collected in super-resolution mode EPU bin2 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 808912 Details: particles from template and TOPAZ trained picking after initial 2D classification to remove junk | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 344606 / Algorithm: FOURIER SPACE Details: cryoSPARC masked local refinement focussed on SIT1 with symmetry expanded particles after 3D classification in RELION Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 112 / Protocol: OTHER / Space: REAL Details: Initial model fitting was peformed in Chimera and model building in COOT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6M18 Pdb chain-ID: C / Accession code: 6M18 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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