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- EMDB-17382: Structure of human SIT1:ACE2 complex (closed PD conformation) bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-17382
TitleStructure of human SIT1:ACE2 complex (closed PD conformation) bound to L-pipecolate
Map datacryoSPARC NU refinement map sharpened with a bfactor of -75 used for model refinement
Sample
  • Complex: SIT1:ACE2 complex
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: Sodium- and chloride-dependent transporter XTRP3
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-alpha-D-glucopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S)-piperidine-2-carboxylic acid
Keywordsamino 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 / tryptophan transport / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / transport across blood-brain barrier / sodium ion transmembrane transport / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / metallocarboxypeptidase activity / Metabolism of Angiotensinogen to Angiotensins / Attachment and Entry / negative regulation of signaling receptor activity / carboxypeptidase activity / 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 / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / 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 / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Neutral amino acid SLC6 transporter / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter ...Neutral amino acid SLC6 transporter / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Angiotensin-converting enzyme 2 / Sodium- and chloride-dependent transporter XTRP3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsLi 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
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/V018051/1 United Kingdom
CitationJournal: To Be Published
Title: Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2
Authors: 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 / Burgess-Brown NA / Dafforn TR / Carpenter EP / Sauer DB
History
DepositionMay 16, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17382.png

Downloads & links

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Map

FileDownload / File: emd_17382.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoSPARC NU refinement map sharpened with a bfactor of -75 used for model refinement
Voxel sizeX=Y=Z: 1.2465 Å
Density
Contour LevelBy AUTHOR: 0.135
Minimum - Maximum-0.6506547 - 1.2325522
Average (Standard dev.)0.0018478454 (±0.029783204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 319.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened NU refinement full map

Fileemd_17382_additional_1.map
Annotationunsharpened NU refinement full map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_17382_half_map_1.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1

Fileemd_17382_half_map_2.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SIT1:ACE2 complex

EntireName: SIT1:ACE2 complex
Components
  • Complex: SIT1:ACE2 complex
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: Sodium- and chloride-dependent transporter XTRP3
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-alpha-D-glucopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S)-piperidine-2-carboxylic acid

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Supramolecule #1: SIT1:ACE2 complex

SupramoleculeName: SIT1:ACE2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 340 KDa

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Macromolecule #1: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.42557 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Sodium- and chloride-dependent transporter XTRP3

MacromoleculeName: Sodium- and chloride-dependent transporter XTRP3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.376258 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: 2-acetamido-2-deoxy-alpha-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-alpha-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NDG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NDG:
2-acetamido-2-deoxy-alpha-D-glucopyranose

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #8: (2S)-piperidine-2-carboxylic acid

MacromoleculeName: (2S)-piperidine-2-carboxylic acid / type: ligand / ID: 8 / Number of copies: 2 / Formula: YCP
Molecular weightTheoretical: 129.157 Da
Chemical component information

ChemComp-YCP:
(2S)-piperidine-2-carboxylic 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 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
25.0 mMTris
150.0 mMsodium chloride
0.02 w/vglyco-diosgenin (GDN)
10.0 mMpipecolic acid
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: grid blotted for 4sec after a 20sec wait time.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 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: 808912
Details: particles from template and TOPAZ trained picking after initial 2D classification to remove junk
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 154699
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6m18


Chain - Chain ID: C / Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot (ver. 0.9.6)
DetailsInitial model fitting was peformed in Chimera and model building in COOT
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 75
Output model

PDB-8p31:
Structure of human SIT1:ACE2 complex (closed PD conformation) bound to L-pipecolate

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