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- EMDB-17076: Human Coronavirus HKU1 spike glycoprotein in complex with an alph... -
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Open data
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Basic information
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Title | Human Coronavirus HKU1 spike glycoprotein in complex with an alpha2,8-linked 9-O-acetylated disialoside (closed state) | |||||||||
![]() | DeepEMhancer sharpened map | |||||||||
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![]() | Virus / Coronavirus / HKU1 / Spike / Glycoprotein / Membrane fusion / Viral protein | |||||||||
Function / homology | ![]() protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / cellular response to nutrient levels / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / 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 / identical protein binding / membrane / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Drulyte I / Hurdiss DL | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 80 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.1 KB 25.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 96.3 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 8 KB | ||
Others | ![]() ![]() ![]() ![]() | 97.4 MB 51.6 MB 95.7 MB 95.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8opmMC ![]() 8ohnC ![]() 8opnC ![]() 8opoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | DeepEMhancer sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1067 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Sharpened map
File | emd_17076_additional_1.map | ||||||||||||
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-Additional map: Unsharpened map
File | emd_17076_additional_2.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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-Half map: Half map A
File | emd_17076_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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-Half map: Half map B
File | emd_17076_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Sample components
-Entire : Trimeric spike glycoprotein
Entire | Name: Trimeric spike glycoprotein |
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Components |
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-Supramolecule #1: Trimeric spike glycoprotein
Supramolecule | Name: Trimeric spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 440 KDa |
-Macromolecule #1: Spike glycoprotein,General control transcription factor GCN4
Macromolecule | Name: Spike glycoprotein,General control transcription factor GCN4 type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 147.770344 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 30 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.3 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Concentration of protein (N-linked glycans not included due to glycan heterogeneity). |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV / Details: BioContinuum Imaging Filter |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 14-1225 / Chain - Source name: Other / Chain - Initial model type: in silico model / Details: Phyre2 |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 114 / Target criteria: Cross-correlation coefficient |
Output model | ![]() PDB-8opm: |