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- EMDB-17077: Human Coronavirus HKU1 spike glycoprotein in complex with an alph... -

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Entry
Database: EMDB / ID: EMD-17077
TitleHuman Coronavirus HKU1 spike glycoprotein in complex with an alpha2,8-linked 9-O-acetylated disialoside (1-up state)
Map dataDeepEMhancer sharpened map
Sample
  • Complex: Trimeric spike glycoprotein
    • Protein or peptide: Spike glycoprotein,General control transcription factor GCN4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVirus / Coronavirus / HKU1 / Spike / Glycoprotein / Membrane fusion / Viral Protein
Function / homology
Function and homology information


protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / endocytosis involved in viral entry into host cell / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / chromatin binding / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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
Similarity search - Domain/homology
Spike glycoprotein / General control transcription factor GCN4
Similarity search - Component
Biological speciesHuman coronavirus HKU1 / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsDrulyte I / Hurdiss DL
Funding support Netherlands, China, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)VI.Veni.202.271 Netherlands
Chinese Scholarship Council2014-03250042 China
CitationJournal: Nature / Year: 2023
Title: Sialoglycan binding triggers spike opening in a human coronavirus.
Authors: Matti F Pronker / Robert Creutznacher / Ieva Drulyte / Ruben J G Hulswit / Zeshi Li / Frank J M van Kuppeveld / Joost Snijder / Yifei Lang / Berend-Jan Bosch / Geert-Jan Boons / Martin Frank ...Authors: Matti F Pronker / Robert Creutznacher / Ieva Drulyte / Ruben J G Hulswit / Zeshi Li / Frank J M van Kuppeveld / Joost Snijder / Yifei Lang / Berend-Jan Bosch / Geert-Jan Boons / Martin Frank / Raoul J de Groot / Daniel L Hurdiss /
Abstract: Coronavirus spike proteins mediate receptor binding and membrane fusion, making them prime targets for neutralizing antibodies. In the cases of severe acute respiratory syndrome coronavirus, severe ...Coronavirus spike proteins mediate receptor binding and membrane fusion, making them prime targets for neutralizing antibodies. In the cases of severe acute respiratory syndrome coronavirus, severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus, spike proteins transition freely between open and closed conformations to balance host cell attachment and immune evasion. Spike opening exposes domain S1, allowing it to bind to proteinaceous receptors, and is also thought to enable protein refolding during membrane fusion. However, with a single exception, the pre-fusion spike proteins of all other coronaviruses studied so far have been observed exclusively in the closed state. This raises the possibility of regulation, with spike proteins more commonly transitioning to open states in response to specific cues, rather than spontaneously. Here, using cryogenic electron microscopy and molecular dynamics simulations, we show that the spike protein of the common cold human coronavirus HKU1 undergoes local and long-range conformational changes after binding a sialoglycan-based primary receptor to domain S1. This binding triggers the transition of S1 domains to the open state through allosteric interdomain crosstalk. Our findings provide detailed insight into coronavirus attachment, with possibilities of dual receptor usage and priming of entry as a means of immune escape.
History
DepositionApr 7, 2023-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17077.png

Downloads & links

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Map

FileDownload / File: emd_17077.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 300 pix.
= 332.01 Å		1.11 Å/pix.
x 300 pix.
= 332.01 Å		1.11 Å/pix.
x 300 pix.
= 332.01 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.073
Minimum - Maximum-0.0046708756 - 1.6564627
Average (Standard dev.)0.0019802833 (±0.026548052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 332.00998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17077_msk_1.map
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Additional map: Unsharpened map

Fileemd_17077_additional_1.map
AnnotationUnsharpened map
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Additional map: Sharpened map

Fileemd_17077_additional_2.map
AnnotationSharpened map
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Half map: Half map A

Fileemd_17077_half_map_1.map
AnnotationHalf map A
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_17077_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : Trimeric spike glycoprotein

EntireName: Trimeric spike glycoprotein
Components
  • Complex: Trimeric spike glycoprotein
    • Protein or peptide: Spike glycoprotein,General control transcription factor GCN4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Trimeric spike glycoprotein

SupramoleculeName: Trimeric spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human coronavirus HKU1 / Strain: Caen1 / Location in cell: membrane
Molecular weightTheoretical: 440 KDa

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Macromolecule #1: Spike glycoprotein,General control transcription factor GCN4

MacromoleculeName: Spike glycoprotein,General control transcription factor GCN4
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 147.770344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAVIGDFN CTNFAINDLN TTIPRISEYV VDVSYGLGTY YILDRVYLNT TILFTGYFPK SGANFRDLS LKGTTKLSTL WYQKPFLSDF NNGIFSRVKN TKLYVNKTLY SEFSTIVIGS VFINNSYTIV VQPHNGVLEI T ACQYTMCE ...String:
MPMGSLQPLA TLYLLGMLVA SVLAVIGDFN CTNFAINDLN TTIPRISEYV VDVSYGLGTY YILDRVYLNT TILFTGYFPK SGANFRDLS LKGTTKLSTL WYQKPFLSDF NNGIFSRVKN TKLYVNKTLY SEFSTIVIGS VFINNSYTIV VQPHNGVLEI T ACQYTMCE YPHTICKSIG SSRNESWHFD KSEPLCLFKK NFTYNVSTDW LYFHFYQERG TFYAYYADSG MPTTFLFSLY LG TLLSHYY VLPLTCNAIS SNTDNETLQY WVTPLSKRQY LLKFDDRGVI TNAVDCSSSF FSEIQCKTKS LLPNTGVYDL SGF TVKPVA TVHRRIPDLP DCDIDKWLNN FNVPSPLNWE RKIFSNCNFN LSTLLRLVHT DSFSCNNFDE SKIYGSCFKS IVLD KFAIP NSRRSDLQLG SSGFLQSSNY KIDTTSSSCQ LYYSLPAINV TINNYNPSSW NRRYGFNNFN LSSHSVVYSR YCFSV NNTF CPCAKPSFAS SCKSHKPPSA SCPIGTNYRS CESTTVLDHT DWCRCSCLPD PITAYDPRSC SQKKSLVGVG EHCAGF GVD EEKCGVLDGS YNVSCLCSTD AFLGWSYDTC VSNNRCNIFS NFILNGINSG TTCSNDLLQP NTEVFTDVCV DYDLYGI TG QGIFKEVSAV YYNSWQNLLY DFNGNIIGFK DFVTNKTYNI FPCYAGRVSA AFHQNASSLA LLYRNLKCSY VLNNISLA T QPYFDSYLGC VFNADNLTDY SVSSCALRMG SGFCVDYNSP SSSSSGGSGS SISASYRFVT FEPFNVSFVN DSIESVGGL YEIKIPTNFT IVGQEEFIQT NSPKVTIDCS LFVCSNYAAC HDLLSEYGTF CDNINSILDE VNGLLDTTQL HVADTLMQGV TLSSNLNTN LHFDVDNINF KSLVGCLGPH CGSSSRSFFE DLLFDKVKLS DVGFVEAYNN CTGGSEIRDL LCVQSFNGIK V LPPILSES QISGYTTAAT VAAMFPPWSA AAGIPFSLNV QYRINGLGVT MDVLNKNQKL IATAFNNALL SIQNGFSATN SA LAKIQSV VNSNAQALNS LLQQLFNKFG AISSSLQEIL SRLDALEAQV QIDRLINGRL TALNAYVSQQ LSDISLVKLG AAL AMEKVN ECVKSQSPRI NFCGNGNHIL SLVQNAPYGL LFMHFSYKPI SFKTVLVSPG LCISGDVGIA PKQGYFIKHN DHWM FTGSS YYYPEPISDK NVVFMNTCSV NFTKAPLVYL NHSVPKLSDF ESELSHWFKN QTSIAPNLTL NLHTINATFL DLLIK RMKQ IEDKIEEIES KQKKIENEIA RIKKIKLVPR GSLEWSHPQF EK

UniProtKB: Spike glycoprotein, General control transcription factor GCN4

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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: 26 / 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

Concentration1.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMTris-HClTris
1.0 mMEDTAEthylenediaminetetraacetic acid
2.5 mMD-biotin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsConcentration of protein (N-linked glycans not included due to glycan heterogeneity).

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 20 eV / Details: BioContinuum Imaging Filter
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4057 / Average exposure time: 2.68 sec. / Average electron dose: 46.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 956697
Startup modelType of model: OTHER / Details: Ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1) / Details: Ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 36048
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6nzk


Chain - Chain ID: A / Chain - Residue range: 14-1225 / Chain - Source name: Other / Chain - Initial model type: in silico model / Details: Phyre2
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 114 / Target criteria: Cross-correlation coefficient
Output model

PDB-8opn:
Human Coronavirus HKU1 spike glycoprotein in complex with an alpha2,8-linked 9-O-acetylated disialoside (1-up state)

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