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Yorodumi- EMDB-33945: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 3 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33945 | |||||||||
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Title | Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 3 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | MERS-CoV / Spike / Glycoprotein / Viral protein | |||||||||
Biological species | Human betacoronavirus 2c EMC/2012 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
Authors | Hsu STD / Chang NE / Weng ZW / Yang TJ / Draczkowski P | |||||||||
Funding support | Taiwan, 1 items
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Citation | Journal: To Be Published Title: GlycoSHIELD: a versatile pipeline to assess glycan impact on protein structures Authors: Gecht M / von Bulow S / Penet C / Hummer G / Hanus C / Sikora M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33945.map.gz | 30.8 MB | EMDB map data format | |
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Header (meta data) | emd-33945-v30.xml emd-33945.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33945_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_33945.png | 21.8 KB | ||
Others | emd_33945_additional_1.map.gz emd_33945_half_map_1.map.gz emd_33945_half_map_2.map.gz | 59.7 MB 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33945 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33945 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33945.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_33945_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33945_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33945_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike
Entire | Name: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike |
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Components |
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-Supramolecule #1: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike
Supramolecule | Name: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human betacoronavirus 2c EMC/2012 |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betacoronavirus 2c EMC/2012 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||
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Buffer | pH: 7.6 Component:
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Vitrification | Cryogen 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.. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 92000 |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2886 / Average electron dose: 40.6 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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