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Yorodumi- EMDB-17380: Structure of human SIT1 bound to L-pipecolate (focussed map / ref... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17380 | |||||||||
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Title | Structure of human SIT1 bound to L-pipecolate (focussed map / refinement) | |||||||||
Map data | Autosharpened cryoSPARC local refinement map used for model refinement | |||||||||
Sample |
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Keywords | amino acid transporter / proline / SLC6A20 / ACE2 / MEMBRANE PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Li HZ / Pike ACW / Chi G / Hansen JS / Lee SG / Rodstrom KEJ / Bushell SR / Speedman D / Evans A / Wang D ...Li HZ / Pike ACW / Chi G / Hansen JS / Lee SG / Rodstrom KEJ / Bushell SR / Speedman D / Evans A / Wang D / He D / Shrestha L / Nasrallah C / Chalk R / Moreira T / MacLean EM / Marsden B / Bountra C / Burgess-Brown NA / Dafforn TR / Carpenter EP / Sauer DB | |||||||||
Funding support | United Kingdom, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17380.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-17380-v30.xml emd-17380.xml | 26.5 KB 26.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17380_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_17380.png | 135.9 KB | ||
Masks | emd_17380_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-17380.cif.gz | 8.2 KB | ||
Others | emd_17380_additional_1.map.gz emd_17380_half_map_1.map.gz emd_17380_half_map_2.map.gz | 32.2 MB 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17380 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17380 | HTTPS FTP |
-Related structure data
Related structure data | 8p2zMC 8p2wC 8p2xC 8p2yC 8p30C 8p31C 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_17380.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Autosharpened cryoSPARC local refinement map used for model refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.2465 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17380_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened full map
File | emd_17380_additional_1.map | ||||||||||||
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Annotation | Unsharpened full map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map1
File | emd_17380_half_map_1.map | ||||||||||||
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Annotation | half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map2
File | emd_17380_half_map_2.map | ||||||||||||
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Annotation | half map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SIT1:ACE2 complex
Entire | Name: SIT1:ACE2 complex |
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Components |
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-Supramolecule #1: SIT1:ACE2 complex
Supramolecule | Name: SIT1:ACE2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 340 KDa |
-Macromolecule #1: Processed angiotensin-converting enzyme 2
Macromolecule | Name: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Details: ACE2 TMD / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 93.42557 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSSSSWLLLS LVAVTAADYK DDDDKSTIEE QAKTFLDKFN HEAEDLFYQS SLASWNYNTN ITEENVQNMN NAGDKWSAFL KEQSTLAQM YPLQEIQNLT VKLQLQALQQ NGSSVLSEDK SKRLNTILNT MSTIYSTGKV CNPDNPQECL LLEPGLNEIM A NSLDYNER ...String: MSSSSWLLLS LVAVTAADYK DDDDKSTIEE QAKTFLDKFN HEAEDLFYQS SLASWNYNTN ITEENVQNMN NAGDKWSAFL KEQSTLAQM YPLQEIQNLT VKLQLQALQQ NGSSVLSEDK SKRLNTILNT MSTIYSTGKV CNPDNPQECL LLEPGLNEIM A NSLDYNER LWAWESWRSE VGKQLRPLYE EYVVLKNEMA RANHYEDYGD YWRGDYEVNG VDGYDYSRGQ LIEDVEHTFE EI KPLYEHL HAYVRAKLMN AYPSYISPIG CLPAHLLGDM WGRFWTNLYS LTVPFGQKPN IDVTDAMVDQ AWDAQRIFKE AEK FFVSVG LPNMTQGFWE NSMLTDPGNV QKAVCHPTAW DLGKGDFRIL MCTKVTMDDF LTAHHEMGHI QYDMAYAAQP FLLR NGANE GFHEAVGEIM SLSAATPKHL KSIGLLSPDF QEDNETEINF LLKQALTIVG TLPFTYMLEK WRWMVFKGEI PKDQW MKKW WEMKREIVGV VEPVPHDETY CDPASLFHVS NDYSFIRYYT RTLYQFQFQE ALCQAAKHEG PLHKCDISNS TEAGQK LFN MLRLGKSEPW TLALENVVGA KNMNVRPLLN YFEPLFTWLK DQNKNSFVGW STDWSPYADQ SIKVRISLKS ALGDKAY EW NDNEMYLFRS SVAYAMRQYF LKVKNQMILF GEEDVRVANL KPRISFNFFV TAPKNVSDII PRTEVEKAIR MSRSRIND A FRLNDNSLEF LGIQPTLGPP NQPPVSIWLI VFGVVMGVIV VGIVILIFTG IRDRKKKNKA RSGENPYASI DISKGENNP GFQNTDDVQT SF UniProtKB: Angiotensin-converting enzyme 2 |
-Macromolecule #2: Sodium- and chloride-dependent transporter XTRP3
Macromolecule | Name: Sodium- and chloride-dependent transporter XTRP3 / 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: 71.376258 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEKARPLWAN SLQFVFACIS YAVGLGNVWR FPYLCQMYGG GSFLVPYIIM LIVEGMPLLY LELAVGQRMR QGSIGAWRTI SPYLSGVGV ASVVVSFFLS MYYNVINAWA FWYLFHSFQD PLPWSVCPLN GNHTGYDEEC EKASSTQYFW YRKTLNISPS L QENGGVQW ...String: MEKARPLWAN SLQFVFACIS YAVGLGNVWR FPYLCQMYGG GSFLVPYIIM LIVEGMPLLY LELAVGQRMR QGSIGAWRTI SPYLSGVGV ASVVVSFFLS MYYNVINAWA FWYLFHSFQD PLPWSVCPLN GNHTGYDEEC EKASSTQYFW YRKTLNISPS L QENGGVQW EPALCLLLAW LVVYLCILRG TESTGKVVYF TASLPYCVLI IYLIRGLTLH GATNGLMYMF TPKIEQLANP KA WINAATQ IFFSLGLGFG SLIAFASYNE PSNNCQKHAI IVSLINSFTS IFASIVTFSI YGFKATFNYE NCLKKVSLLL TNT FDLEDG FLTASNLEQV KGYLASAYPS KYSEMFPQIK NCSLESELDT AVQGTGLAFI VYTEAIKNME VSQLWSVLYF FMLL MLGIG SMLGNTAAIL TPLTDSKIIS SHLPKEAISG LVCLVNCAIG MVFTMEAGNY WFDIFNDYAA TLSLLLIVLV ETIAV CYVY GLRRFESDLK AMTGRAVSWY WKVMWAGVSP LLIVSLFVFY LSDYILTGTL KYQAWDASQG QLVTKDYPAY ALAVIG LLV ASSTMCIPLA ALGTFVQRRL KRGDADPVAA ENLYFQSHHH HHHHHHHGSA WSHPQFEKGG GSGGGSGGSA WSHPQFE K UniProtKB: Sodium- and chloride-dependent transporter XTRP3 |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: (2S)-piperidine-2-carboxylic acid
Macromolecule | Name: (2S)-piperidine-2-carboxylic acid / type: ligand / ID: 4 / Number of copies: 1 / Formula: YCP |
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Molecular weight | Theoretical: 129.157 Da |
Chemical component information | ChemComp-YCP: |
-Macromolecule #5: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | ||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: grid blotted for 4sec after a 20sec wait time. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 13194 / Average exposure time: 1.77 sec. / Average electron dose: 50.0 e/Å2 Details: Images were collected in super-resolution mode EPU bin2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: C / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Initial model fitting was peformed in Chimera and model building in COOT |
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 112 |
Output model | PDB-8p2z: |