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- EMDB-33945: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-33945
TitleCryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 3
Map data
Sample
  • Organelle or cellular component: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike
    • Protein or peptide: Spike glycoprotein
KeywordsMERS-CoV / Spike / Glycoprotein / Viral protein
Biological speciesHuman betacoronavirus 2c EMC/2012
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 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-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33945.png

Downloads & links

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Map

FileDownload / File: emd_33945.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.88 Å/pix.
x 128 pix.
= 240.64 Å		1.88 Å/pix.
x 128 pix.
= 240.64 Å		1.88 Å/pix.
x 128 pix.
= 240.64 Å

Surface

Projections

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Images are generated by Spider.

Voxel size
XYZ
EMDB info.1.11.11.1
CCP4 map header1.881.881.88
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.55573606 - 1.5478563
Average (Standard dev.)-0.0069956854 (±0.11784681)
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_33945_additional_1.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Half map: #1

Fileemd_33945_half_map_1.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

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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: all
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 / Enantiomer: LEVO
Source (natural)Organism: Human betacoronavirus 2c EMC/2012
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSWFILVLL GSGLICVSAS YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYSQ DVKQFANGFV VRIGAAANST GTVIISPSTS ATIRKIYPAF MLGSSVGNFS DGKMGRFFNH ...String:
MDSWFILVLL GSGLICVSAS YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYSQ DVKQFANGFV VRIGAAANST GTVIISPSTS ATIRKIYPAF MLGSSVGNFS DGKMGRFFNH TLVLLPDGCG TLLRAFYCIL EPRSGNHCPA GNSYTSFATY HTPATDCSDG NYNRNASLNS FKEYFNLRNC TFMYTYNITE DEILEWFGIT QTAQGVHLFS SRYVDLYGGN MFQFATLPVY DTIKYYSIIP HSIRSIQSDR KAWAAFYVYK LQPLTFLLDF SVDGYIRRAI DCGFNDLSQL HCSYESFDVE SGVYSVSSFE AKPSGSVVEQ AEGVECDFSP LLSGTPPQVY NFKRLVFTNC NYNLTKLLSL FSVNDFTCSQ ISPAAIASNC YSSLILDYFS YPLSMKSDLS VSSAGPISQF NYKQSFSNPT CLILATVPHN LTTITKPLKY SYINKCSRLL SDDRTEVPQL VNANQYSPCV SIVPSTVWED GDYYRKQLSP LEGGGWLVAS GSTVAMTEQL QMGFGITVQY GTDTNSVCPK LEFANDTKIA SQLGNCVEYS LYGVSGRGVF QNCTAVGVRQ QRFVYDAYQN LVGYYSDDGN YYCLRACVSV PVSVIYDKET KTHATLFGSV ACEHISSTMS QYSRSTRSML KRRDSTYGPL QTPVGCVLGL VNSSLFVEDC KLPLGQSLCA LPDTPSTLTP ASVGSVPGEM RLASIAFNHP IQVDQLNSSY FKLSIPTNFS FGVTQEYIQT TIQKVTVDCK QYVCNGFQKC EQLLREYGQF CSKINQALHG ANLRQDDSVR NLFASVKSSQ SSPIIPGFGG DFNLTLLEPV SISTGSRSAR SAIEDLLFDK VTIADPGYMQ GYDDCMQQGP ASARDLICAQ YVAGYKVLPP LMDVNMEAAY TSSLLGSIAG VGWTAGLSSF AAIPFAQSIF YRLNGVGITQ QVLSENQKLI ANKFNQALGA MQTGFTTTNE AFQKVQDAVN NNAQALSKLA SELSNTFGAI SASIGDIIQR LDPPEQDAQI DRLINGRLTT LNAFVAQQLV RSESAALSAQ LAKDKVNECV KAQSKRSGFC GQGTHIVSFV VNAPNGLYFM HVGYYPSNHI EVVSAYGLCD AANPTNCIAP VNGYFIKTNN TRIVDEWSYT GSSFYAPEPI TSLNTKYVAP QVTYQNISTN LPPPLLGNST GIDFQDELDE FFKNVSTSIP NFGSLTQINT TLLDLTYEML SLQQVVKALN ESYIDLKELG NYTYEFGSGG YIPEAPRDGQ AYVRKDGEWV LLSTFLKGQD NSADIQHSGR PLESRGPFEQ KLISEEDLNM HTGHHHHHH

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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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 36358
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

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