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- EMDB-33653: SIT1-ACE2-BA.5 RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-33653
TitleSIT1-ACE2-BA.5 RBD
Map data
Sample
  • Complex: SIT1-ACE2-BA.5 RBD
    • Complex: SIT1
      • Protein or peptide: SIT1
    • Complex: ACE2 FL
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: RBD of BA.5 spike
      • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: ZINC ION
KeywordsSARS-Cov-2 / VIRAL PROTEIN / VIRAL PROTEIN-HYDROLASE complex / RECOMBINATION
Function / homology
Function and homology information


proline:sodium symporter activity / L-isoleucine transmembrane transporter activity / solute:sodium symporter activity / 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) / amino-acid betaine transport / proline import across plasma membrane / L-proline transmembrane transporter activity ...proline:sodium symporter activity / L-isoleucine transmembrane transporter activity / solute:sodium symporter activity / 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) / amino-acid betaine transport / 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 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 / 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 / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / 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 2. / 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. ...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 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. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2 / Sodium- and chloride-dependent transporter XTRP3
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShen YP / Li YN / Zhang YY / Yan RH
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509301 China
CitationJournal: Cell Discov / Year: 2022
Title: Structures of ACE2-SIT1 recognized by Omicron variants of SARS-CoV-2.
Authors: Yaping Shen / Jianhui Wang / Yaning Li / Yuanyuan Zhang / Ruilin Tian / Renhong Yan /
History
DepositionJun 21, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33653.png

Downloads & links

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Map

FileDownload / File: emd_33653.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: 0.013
Minimum - Maximum-0.045836736 - 0.0959751
Average (Standard dev.)0.000050510567 (±0.0028815428)
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_33653_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_33653_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 : SIT1-ACE2-BA.5 RBD

EntireName: SIT1-ACE2-BA.5 RBD
Components
  • Complex: SIT1-ACE2-BA.5 RBD
    • Complex: SIT1
      • Protein or peptide: SIT1
    • Complex: ACE2 FL
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: RBD of BA.5 spike
      • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: SIT1-ACE2-BA.5 RBD

SupramoleculeName: SIT1-ACE2-BA.5 RBD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: SIT1

SupramoleculeName: SIT1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: ACE2 FL

SupramoleculeName: ACE2 FL / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #4: RBD of BA.5 spike

SupramoleculeName: RBD of BA.5 spike / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: SIT1

MacromoleculeName: SIT1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.22482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGPDEVDASG RMEKARPLWA NSLQFVFACI SYAVGLGNVW RFPYLCQMYG GGSFLVPYII MLIVEGMPLL YLELAVGQR MRQGSIGAWR TISPYLSGVG VASVVVSFFL SMYYNVINAW AFWYLFHSFQ DPLPWSVCPL NGNHTGYDEE C EKASSTQY ...String:
MADYKDDDDK SGPDEVDASG RMEKARPLWA NSLQFVFACI SYAVGLGNVW RFPYLCQMYG GGSFLVPYII MLIVEGMPLL YLELAVGQR MRQGSIGAWR TISPYLSGVG VASVVVSFFL SMYYNVINAW AFWYLFHSFQ DPLPWSVCPL NGNHTGYDEE C EKASSTQY FWYRKTLNIS PSLQENGGVQ WEPALCLLLA WLVVYLCILR GTESTGKVVY FTASLPYCVL IIYLIRGLTL HG ATNGLMY MFTPKIEQLA NPKAWINAAT QIFFSLGLGF GSLIAFASYN EPSNNCQKHA IIVSLINSFT SIFASIVTFS IYG FKATFN YENCLKKVSL LLTNTFDLED GFLTASNLEQ VKGYLASAYP SKYSEMFPQI KNCSLESELD TAVQGTGLAF IVYT EAIKN MEVSQLWSVL YFFMLLMLGI GSMLGNTAAI LTPLTDSKII SSHLPKEAIS GLVCLVNCAI GMVFTMEAGN YWFDI FNDY AATLSLLLIV LVETIAVCYV YGLRRFESDL KAMTGRAVSW YWKVMWAGVS PLLIVSLFVF YLSDYILTGT LKYQAW DAS QGQLVTKDYP AYALAVIGLL VASSTMCIPL AALGTFVQRR LKRGDADPVA

UniProtKB: Sodium- and chloride-dependent transporter XTRP3

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Macromolecule #2: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 2 / 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 #3: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 28.492443 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGVKVLFALI CIAVAEAGTR VQPTESIVRF PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLN DLCFTNVYAD SFVIRGNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVGGN YNYRYRLFRK S NLKPFERD ...String:
MGVKVLFALI CIAVAEAGTR VQPTESIVRF PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLN DLCFTNVYAD SFVIRGNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVGGN YNYRYRLFRK S NLKPFERD ISTEIYQAGN KPCNGVAGVN CYFPLQSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CV NFLEHHH HHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 6 / Number of copies: 6 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 398746
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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