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- EMDB-35256: ACE2-B0AT1 complex bound with methionine -

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Basic information

Entry
Database: EMDB / ID: EMD-35256
TitleACE2-B0AT1 complex bound with methionine
Map data
Sample
  • Complex: ACE2-B0AT1 complex bound with methionine
    • 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: METHIONINE
Keywordstransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / neutral amino acid transport / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / symporter activity / Na+/Cl- dependent neurotransmitter transporters / amino acid transport / positive regulation of amino acid transport ...Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / neutral amino acid transport / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / symporter 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 / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / sodium ion transmembrane transport / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of signaling receptor activity / carboxypeptidase activity / Attachment and Entry / positive regulation of cardiac muscle contraction / viral life cycle / regulation of cytokine production / blood vessel diameter maintenance / response to nutrient / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / 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 / identical protein binding / membrane / 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: 3.1 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_35256.png

Downloads & links

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Map

FileDownload / File: emd_35256.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-0.055565946 - 0.11108136
Average (Standard dev.)0.00008917193 (±0.0030891544)
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_35256_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_35256_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 methionine

EntireName: ACE2-B0AT1 complex bound with methionine
Components
  • Complex: ACE2-B0AT1 complex bound with methionine
    • 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: METHIONINE

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Supramolecule #1: ACE2-B0AT1 complex bound with methionine

SupramoleculeName: ACE2-B0AT1 complex bound with methionine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.549078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TIEEQAKTFL DKFNHEAEDL FYQSSLASWN YNTNITEENV QNMNNAGDKW SAFLKEQSTL AQMYPLQEIQ NLTVKLQLQA LQQNGSSVL SEDKSKRLNT ILNTMSTIYS TGKVCNPDNP QECLLLEPGL NEIMANSLDY NERLWAWESW RSEVGKQLRP L YEEYVVLK ...String:
TIEEQAKTFL DKFNHEAEDL FYQSSLASWN YNTNITEENV QNMNNAGDKW SAFLKEQSTL AQMYPLQEIQ NLTVKLQLQA LQQNGSSVL SEDKSKRLNT ILNTMSTIYS TGKVCNPDNP QECLLLEPGL NEIMANSLDY NERLWAWESW RSEVGKQLRP L YEEYVVLK NEMARANHYE DYGDYWRGDY EVNGVDGYDY SRGQLIEDVE HTFEEIKPLY EHLHAYVRAK LMNAYPSYIS PI GCLPAHL LGDMWGRFWT NLYSLTVPFG QKPNIDVTDA MVDQAWDAQR IFKEAEKFFV SVGLPNMTQG FWENSMLTDP GNV QKAVCH PTAWDLGKGD FRILMCTKVT MDDFLTAHHE MGHIQYDMAY AAQPFLLRNG ANEGFHEAVG EIMSLSAATP KHLK SIGLL SPDFQEDNET EINFLLKQAL TIVGTLPFTY MLEKWRWMVF KGEIPKDQWM KKWWEMKREI VGVVEPVPHD ETYCD PASL FHVSNDYSFI RYYTRTLYQF QFQEALCQAA KHEGPLHKCD ISNSTEAGQK LFNMLRLGKS EPWTLALENV VGAKNM NVR PLLNYFEPLF TWLKDQNKNS FVGWSTDWSP YADQSIKVRI SLKSALGDKA YEWNDNEMYL FRSSVAYAMR QYFLKVK NQ MILFGEEDVR VANLKPRISF NFFVTAPKNV SDIIPRTEVE KAIRMSRSRI NDAFRLNDNS LEFLGIQPTL GPPNQPPV S IWLIVFGVVM GVIVVGIVIL IFTGIRDR

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: 73.12618 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGPDEVDASG RVRLVLPNPG LDARIPSLAE LETIEQEEAS SRPKWDNKAQ YMLTCLGFCV GLGNVWRFPY LCQSHGGGA FMIPFLILLV LEGIPLLYLE FAIGQRLRRG SLGVWSSIHP ALKGLGLASM LTSFMVGLYY NTIISWIMWY L FNSFQEPL ...String:
MADYKDDDDK SGPDEVDASG RVRLVLPNPG LDARIPSLAE LETIEQEEAS SRPKWDNKAQ YMLTCLGFCV GLGNVWRFPY LCQSHGGGA FMIPFLILLV LEGIPLLYLE FAIGQRLRRG SLGVWSSIHP ALKGLGLASM LTSFMVGLYY NTIISWIMWY L FNSFQEPL PWSDCPLNEN QTGYVDECAR SSPVDYFWYR ETLNISTSIS DSGSIQWWML LCLACAWSVL YMCTIRGIET TG KAVYITS TLPYVVLTIF LIRGLTLKGA TNGIVFLFTP NVTELAQPDT WLDAGAQVFF SFSLAFGGLI SFSSYNSVHN NCE KDSVIV SIINGFTSVY VAIVVYSVIG FRATQRYDDC FSTNILTLIN GFDLPEGNVT QENFVDMQQR CNASDPAAYA QLVF QTCDI NAFLSEAVEG TGLAFIVFTE AITKMPLSPL WSVLFFIMLF CLGLSSMFGN MEGVVVPLQD LRVIPPKWPK EVLTG LICL GTFLIGFIFT LNSGQYWLSL LDSYAGSIPL LIIAFCEMFS VVYVYGVDRF NKDIEFMIGH KPNIFWQVTW RVVSPL LML IIFLFFFVVE VSQELTYSIW DPGYEEFPKS QKISYPNWVY VVVVIVAGVP SLTIPGYAIY KLIRNHCQKP GDHQGLV ST LSTASMNGDL K

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: METHIONINE

MacromoleculeName: METHIONINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: MET
Molecular weightTheoretical: 149.211 Da
Chemical component information

ChemComp-MET:
METHIONINE

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 244699
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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