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- EMDB-33947: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-33947
TitleCryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1
Map data
Sample
  • Organelle or cellular component: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMERS-CoV / Spike / Glycoprotein / Viral protein
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane ...host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / 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 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
Biological speciesHuman betacoronavirus 2c EMC/2012
Methodsingle particle reconstruction / cryo EM / Resolution: 4.96 Å
AuthorsHsu STD / Chang NE / Weng ZW / Yang TJ / Draczkowski P
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Cell / Year: 2024
Title: Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
Authors: Yu-Xi Tsai / Ning-En Chang / Klaus Reuter / Hao-Ting Chang / Tzu-Jing Yang / Sören von Bülow / Vidhi Sehrawat / Noémie Zerrouki / Matthieu Tuffery / Michael Gecht / Isabell Louise ...Authors: Yu-Xi Tsai / Ning-En Chang / Klaus Reuter / Hao-Ting Chang / Tzu-Jing Yang / Sören von Bülow / Vidhi Sehrawat / Noémie Zerrouki / Matthieu Tuffery / Michael Gecht / Isabell Louise Grothaus / Lucio Colombi Ciacchi / Yong-Sheng Wang / Min-Feng Hsu / Kay-Hooi Khoo / Gerhard Hummer / Shang-Te Danny Hsu / Cyril Hanus / Mateusz Sikora /
Abstract: Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain ...Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.
History
DepositionJul 29, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33947.png

Downloads & links

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Map

FileDownload / File: emd_33947.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.44537678 - 1.4884906
Average (Standard dev.)-0.0054555847 (±0.11763734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_33947_additional_1.map
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Half map: #2

Fileemd_33947_half_map_1.map
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Histogram

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Half map: #1

Fileemd_33947_half_map_2.map
Projections & Slices
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Sample components

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Entire : recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike

EntireName: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike
Components
  • Organelle or cellular component: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike

SupramoleculeName: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human betacoronavirus 2c EMC/2012

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human betacoronavirus 2c EMC/2012
Molecular weightTheoretical: 150.654438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSWFILVLL GSGLICVSAS YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYV YSAGHATGTT PQKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF S DGKMGRFF ...String:
MDSWFILVLL GSGLICVSAS YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYV YSAGHATGTT PQKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF S DGKMGRFF NHTLVLLPDG CGTLLRAFYC ILEPRSGNHC PAGNSYTSFA TYHTPATDCS DGNYNRNASL NSFKEYFNLR NC TFMYTYN ITEDEILEWF GITQTAQGVH LFSSRYVDLY GGNMFQFATL PVYDTIKYYS IIPHSIRSIQ SDRKAWAAFY VYK LQPLTF LLDFSVDGYI RRAIDCGFND LSQLHCSYES FDVESGVYSV SSFEAKPSGS VVEQAEGVEC DFSPLLSGTP PQVY NFKRL VFTNCNYNLT KLLSLFSVND FTCSQISPAA IASNCYSSLI LDYFSYPLSM KSDLSVSSAG PISQFNYKQS FSNPT CLIL ATVPHNLTTI TKPLKYSYIN KCSRLLSDDR TEVPQLVNAN QYSPCVSIVP STVWEDGDYY RKQLSPLEGG GWLVAS GST VAMTEQLQMG FGITVQYGTD TNSVCPKLEF ANDTKIASQL GNCVEYSLYG VSGRGVFQNC TAVGVRQQRF VYDAYQN LV GYYSDDGNYY CLRACVSVPV SVIYDKETKT HATLFGSVAC EHISSTMSQY SRSTRSMLKR RDSTYGPLQT PVGCVLGL V NSSLFVEDCK LPLGQSLCAL PDTPSTLTPA SVGSVPGEMR LASIAFNHPI QVDQLNSSYF KLSIPTNFSF GVTQEYIQT TIQKVTVDCK QYVCNGFQKC EQLLREYGQF CSKINQALHG ANLRQDDSVR NLFASVKSSQ SSPIIPGFGG DFNLTLLEPV SISTGSRSA RSAIEDLLFD KVTIADPGYM QGYDDCMQQG PASARDLICA QYVAGYKVLP PLMDVNMEAA YTSSLLGSIA G VGWTAGLS SFAAIPFAQS IFYRLNGVGI TQQVLSENQK LIANKFNQAL GAMQTGFTTT NEAFQKVQDA VNNNAQALSK LA SELSNTF GAISASIGDI IQRLDPPEQD AQIDRLINGR LTTLNAFVAQ QLVRSESAAL SAQLAKDKVN ECVKAQSKRS GFC GQGTHI VSFVVNAPNG LYFMHVGYYP SNHIEVVSAY GLCDAANPTN CIAPVNGYFI KTNNTRIVDE WSYTGSSFYA PEPI TSLNT KYVAPQVTYQ NISTNLPPPL LGNSTGIDFQ DELDEFFKNV STSIPNFGSL TQINTTLLDL TYEMLSLQQV VKALN ESYI DLKELGNYTY EFGSGGYIPE APRDGQAYVR KDGEWVLLST FLKGQDNSAD IQHSGRPLES RGPFEQKLIS EEDLNM HTG HHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 19 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration0.5 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
50.0 mMTristris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride
0.02 %NaN3sodium azide
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: blot for 2.5 seconds before plunging; blot force: -1; waiting time: 30s..

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2886 / Average electron dose: 40.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 92000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1679870
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 60257
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7ymy:
Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1

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