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- EMDB-43224: Structure of the HKU1 RBD bound to the human TMPRSS2 receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-43224
TitleStructure of the HKU1 RBD bound to the human TMPRSS2 receptor
Map data
Sample
  • Complex: HKU1 RBD bound to the human TMPRSS2 receptor
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Transmembrane protease serine 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike glycoprotein / fusion protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / inhibitor / VIRAL PROTEIN
Function / homology
Function and homology information


transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / endocytosis involved in viral entry into host cell / viral translation / Induction of Cell-Cell Fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / endocytosis involved in viral entry into host cell / viral translation / Induction of Cell-Cell Fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. ...Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Transmembrane protease serine 2 / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Human coronavirus HKU1 (isolate N1)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPark YJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158186 United States
CitationJournal: To Be Published
Title: Human coronavirus HKU1 recognition of the TMPRSS2 host receptor
Authors: Park YJ / Veesler D
History
DepositionDec 27, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43224.png

Downloads & links

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Map

FileDownload / File: emd_43224.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-6.9582844 - 10.827133999999999
Average (Standard dev.)-0.000023198552 (±0.12638311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_43224_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43224_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_43224_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 : HKU1 RBD bound to the human TMPRSS2 receptor

EntireName: HKU1 RBD bound to the human TMPRSS2 receptor
Components
  • Complex: HKU1 RBD bound to the human TMPRSS2 receptor
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Transmembrane protease serine 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HKU1 RBD bound to the human TMPRSS2 receptor

SupramoleculeName: HKU1 RBD bound to the human TMPRSS2 receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus HKU1 (isolate N1)
Molecular weightTheoretical: 37.321785 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTRIPDLPDC DIDKWLNNFN VPSPLNWERK IFSNCNFNLS TLLRLVHTDS FSCNNFDES KIYGSCFKSI VLDKFAIPNS RRSDLQLGSS GFLQSSNYKI DTTSSSCQLY YSLPAINVTI NNYNPSSWNR R YGFNNFNL ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTRIPDLPDC DIDKWLNNFN VPSPLNWERK IFSNCNFNLS TLLRLVHTDS FSCNNFDES KIYGSCFKSI VLDKFAIPNS RRSDLQLGSS GFLQSSNYKI DTTSSSCQLY YSLPAINVTI NNYNPSSWNR R YGFNNFNL SSHSVVYSRY CFSVNNTFCP CAKPSFASSC KSHKPPSASC PIGTNYRSCE STTVLDHTDW CRCSCLPDPI TA YDPRSCS QKKSLVGVGE HCAGFGVDEE KCGVLDGSYN VSCLCSTDAF LGWSYDTCVS NNRCNIFSNF ILNGINSGTT CSN DLLQPN TGGSHHHHHH HH

UniProtKB: Spike glycoprotein

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Macromolecule #2: Transmembrane protease serine 2

MacromoleculeName: Transmembrane protease serine 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: transmembrane protease serine 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.232004 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKWVTFISLL FLFSSAYSMG SKCSNSGIEC DSSGTCINPS NWCDGVSHCP GGEDENRCVR LYGPNFILQV YSSQRKSWHP VCQDDWNEN YGRAACRDMG YKNNFYSSQG IVDDSGSTSF MKLNTSAGNV DIYKKLYHSD ACSSKAVVSL RCIACGVNLN D DDDKIVGG ...String:
MKWVTFISLL FLFSSAYSMG SKCSNSGIEC DSSGTCINPS NWCDGVSHCP GGEDENRCVR LYGPNFILQV YSSQRKSWHP VCQDDWNEN YGRAACRDMG YKNNFYSSQG IVDDSGSTSF MKLNTSAGNV DIYKKLYHSD ACSSKAVVSL RCIACGVNLN D DDDKIVGG ESALPGAWPW QVSLHVQNVH VCGGSIITPE WIVTAAHCVE KPLNNPWHWT AFAGILRQSF MFYGAGYQVE KV ISHPNYD SKTKNNDIAL MKLQKPLTFN DLVKPVCLPN PGMMLQPEQL CWISGWGATE EKGKTSEVLN AAKVLLIETQ RCN SRYVYD NLITPAMICA GFLQGNVDSC QGDAGGPLVC SKNNIWWLIG DTSWGSGCAK AYRPGVYGNV MVFTDWIYRQ MRAD GDDDD KSGHHHHHHH H

UniProtKB: Transmembrane protease serine 2

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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: 3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
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: 3.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 810357

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