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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 transport of neurotransmitters by SLC6A19 causes Hartnup disorder (HND) / Defective transport of amino acids by SLC6A19 causes Hartnup disorder (HND) / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / symporter activity / amino acid transmembrane transporter activity / SLC-mediated transport of neurotransmitters / positive regulation of amino acid transport / angiotensin-converting enzyme 2 ...Defective transport of neurotransmitters by SLC6A19 causes Hartnup disorder (HND) / Defective transport of amino acids by SLC6A19 causes Hartnup disorder (HND) / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / symporter activity / amino acid transmembrane transporter activity / SLC-mediated transport of neurotransmitters / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / amino acid transport / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of systemic arterial blood pressure by renin-angiotensin / maternal process involved in female pregnancy / regulation of cardiac conduction / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / Attachment and Entry / viral life cycle / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction / response to nutrient / regulation of cytokine production / blood vessel diameter maintenance / sodium ion transmembrane transport / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / membrane fusion / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / apical plasma membrane / cilium / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / cell surface / negative regulation of transcription by RNA polymerase II / : / extracellular exosome / extracellular region / zinc ion binding / 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 domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A ...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 domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing 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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
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

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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

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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

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

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Image processing

Startup modelType of model: NONE
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
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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