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- EMDB-35255: ACE2-B0AT1 complex bound with glutamine -

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Basic information

Entry
Database: EMDB / ID: EMD-35255
TitleACE2-B0AT1 complex bound with glutamine
Map data
Sample
  • Complex: ACE2-B0AT1 complex bound with glutamine
    • Protein or peptide: Angiotensin-converting enzyme 2
    • Protein or peptide: Sodium-dependent neutral amino acid transporter B(0)AT1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: GLUTAMINE
Keywordstransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / amino acid transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / symporter activity / amino acid transport / positive regulation of amino acid transport / angiotensin-converting enzyme 2 ...Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / amino acid transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / symporter activity / 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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / sodium ion transmembrane transport / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / Attachment and Entry / negative regulation of signaling receptor activity / carboxypeptidase activity / regulation of cytokine production / positive regulation of cardiac muscle contraction / viral life cycle / blood vessel diameter maintenance / response to nutrient / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / cilium / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / metallopeptidase activity / 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 / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Neutral amino acid SLC6 transporter / 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. ...Neutral amino acid SLC6 transporter / 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
Sodium-dependent neutral amino acid transporter B(0)AT1 / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi YN / Zhang YY / Shen YP / Yan RH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92169204 China
CitationJournal: Cell Discov / Year: 2023
Title: Structural insight into the substrate recognition and transport mechanism of amino acid transporter complex ACE2-BAT1 and ACE2-SIT1.
Authors: Yaning Li / Yiming Chen / Yuanyuan Zhang / Yaping Shen / Kangtai Xu / Yaqi Liu / Zilong Wang / Renhong Yan /
History
DepositionFeb 6, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35255.png

Downloads & links

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Map

FileDownload / File: emd_35255.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.054988768 - 0.10120503
Average (Standard dev.)0.00017458483 (±0.0029179403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 313.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35255_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35255_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ACE2-B0AT1 complex bound with glutamine

EntireName: ACE2-B0AT1 complex bound with glutamine
Components
  • Complex: ACE2-B0AT1 complex bound with glutamine
    • Protein or peptide: Angiotensin-converting enzyme 2
    • Protein or peptide: Sodium-dependent neutral amino acid transporter B(0)AT1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: GLUTAMINE

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Supramolecule #1: ACE2-B0AT1 complex bound with glutamine

SupramoleculeName: ACE2-B0AT1 complex bound with glutamine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.379828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRSSSSWLLL SLVAVTAAWS HPQFEKQSTI EEQAKTFLDK FNHEAEDLFY QSSLASWNYN TNITEENVQN MNNAGDKWSA FLKEQSTLA QMYPLQEIQN LTVKLQLQAL QQNGSSVLSE DKSKRLNTIL NTMSTIYSTG KVCNPDNPQE CLLLEPGLNE I MANSLDYN ...String:
MRSSSSWLLL SLVAVTAAWS HPQFEKQSTI EEQAKTFLDK FNHEAEDLFY QSSLASWNYN TNITEENVQN MNNAGDKWSA FLKEQSTLA QMYPLQEIQN LTVKLQLQAL QQNGSSVLSE DKSKRLNTIL NTMSTIYSTG KVCNPDNPQE CLLLEPGLNE I MANSLDYN ERLWAWESWR SEVGKQLRPL YEEYVVLKNE MARANHYEDY GDYWRGDYEV NGVDGYDYSR GQLIEDVEHT FE EIKPLYE HLHAYVRAKL MNAYPSYISP IGCLPAHLLG DMWGRFWTNL YSLTVPFGQK PNIDVTDAMV DQAWDAQRIF KEA EKFFVS VGLPNMTQGF WENSMLTDPG NVQKAVCHPT AWDLGKGDFR ILMCTKVTMD DFLTAHHEMG HIQYDMAYAA QPFL LRNGA NEGFHEAVGE IMSLSAATPK HLKSIGLLSP DFQEDNETEI NFLLKQALTI VGTLPFTYML EKWRWMVFKG EIPKD QWMK KWWEMKREIV GVVEPVPHDE TYCDPASLFH VSNDYSFIRY YTRTLYQFQF QEALCQAAKH EGPLHKCDIS NSTEAG QKL FNMLRLGKSE PWTLALENVV GAKNMNVRPL LNYFEPLFTW LKDQNKNSFV GWSTDWSPYA DQSIKVRISL KSALGDK AY EWNDNEMYLF RSSVAYAMRQ YFLKVKNQMI LFGEEDVRVA NLKPRISFNF FVTAPKNVSD IIPRTEVEKA IRMSRSRI N DAFRLNDNSL EFLGIQPTLG PPNQPPVSIW LIVFGVVMGV IVVGIVILIF TGIRDRKKKN KARSGENPYA SIDISKGEN NPGFQNTDDV QTSFLEHHHH HHHHHH

UniProtKB: Angiotensin-converting enzyme 2

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Macromolecule #2: Sodium-dependent neutral amino acid transporter B(0)AT1

MacromoleculeName: Sodium-dependent neutral amino acid transporter B(0)AT1
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.012609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VLPNPGLDAR IPSLAELETI EQEEASSRPK WDNKAQYMLT CLGFCVGLGN VWRFPYLCQS HGGGAFMIPF LILLVLEGIP LLYLEFAIG QRLRRGSLGV WSSIHPALKG LGLASMLTSF MVGLYYNTII SWIMWYLFNS FQEPLPWSDC PLNENQTGYV D ECARSSPV ...String:
VLPNPGLDAR IPSLAELETI EQEEASSRPK WDNKAQYMLT CLGFCVGLGN VWRFPYLCQS HGGGAFMIPF LILLVLEGIP LLYLEFAIG QRLRRGSLGV WSSIHPALKG LGLASMLTSF MVGLYYNTII SWIMWYLFNS FQEPLPWSDC PLNENQTGYV D ECARSSPV DYFWYRETLN ISTSISDSGS IQWWMLLCLA CAWSVLYMCT IRGIETTGKA VYITSTLPYV VLTIFLIRGL TL KGATNGI VFLFTPNVTE LAQPDTWLDA GAQVFFSFSL AFGGLISFSS YNSVHNNCEK DSVIVSIING FTSVYVAIVV YSV IGFRAT QRYDDCFSTN ILTLINGFDL PEGNVTQENF VDMQQRCNAS DPAAYAQLVF QTCDINAFLS EAVEGTGLAF IVFT EAITK MPLSPLWSVL FFIMLFCLGL SSMFGNMEGV VVPLQDLRVI PPKWPKEVLT GLICLGTFLI GFIFTLNSGQ YWLSL LDSY AGSIPLLIIA FCEMFSVVYV YGVDRFNKDI EFMIGHKPNI FWQVTWRVVS PLLMLIIFLF FFVVEVSQEL TYSIWD PGY EEFPKSQKIS YPNWVYVVVV IVAGVPSLTI PGYAIYKLIR NH

UniProtKB: Sodium-dependent neutral amino acid transporter B(0)AT1

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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: GLUTAMINE

MacromoleculeName: GLUTAMINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GLN
Molecular weightTheoretical: 146.144 Da
Chemical component information

ChemComp-GLN:
GLUTAMINE / Glutamine

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 222017
FSC plot (resolution estimation)

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