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Yorodumi- EMDB-41152: Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus SZ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41152 | |||||||||
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Title | Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus SZ3 in Closed Conformation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Spike / Glycoprotein / Coronavirus / VIRAL PROTEIN | |||||||||
Biological species | Civet SARS CoV SZ3/2003 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.11 Å | |||||||||
Authors | Bostina M / Hills FR / Eruera A | |||||||||
Funding support | New Zealand, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM reveals variation in structural motifs within animal SARS-related coronavirus spike proteins Authors: Bostina M / Hills FR / Eruera A | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41152.map.gz | 123.4 MB | EMDB map data format | |
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Header (meta data) | emd-41152-v30.xml emd-41152.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_41152.png | 64 KB | ||
Filedesc metadata | emd-41152.cif.gz | 6.3 KB | ||
Others | emd_41152_half_map_1.map.gz emd_41152_half_map_2.map.gz | 226.8 MB 226.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41152 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41152 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41152.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41152_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41152_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Civet SARS CoV SZ3/2003
Entire | Name: Civet SARS CoV SZ3/2003 (virus) |
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Components |
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-Supramolecule #1: Civet SARS CoV SZ3/2003
Supramolecule | Name: Civet SARS CoV SZ3/2003 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 231513 / Sci species name: Civet SARS CoV SZ3/2003 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Civet SARS CoV SZ3/2003 (virus) |
Molecular weight | Theoretical: 122.511094 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: LDRCTTFDDV QAPNYTQHTS SMRGVYYPDE IFRSDTLYLT QDLFLPFYSN VTGFHTINHT FDNPVIPFKD GIYFAATEKS NVVRGWVFG STMNNKSQSV IIINNSTNVV IRACNFELCD NPFFAVSKPM GTQTHTMIFD NAFNCTFEYI SDAFSLDVSE K SGNFKHLR ...String: LDRCTTFDDV QAPNYTQHTS SMRGVYYPDE IFRSDTLYLT QDLFLPFYSN VTGFHTINHT FDNPVIPFKD GIYFAATEKS NVVRGWVFG STMNNKSQSV IIINNSTNVV IRACNFELCD NPFFAVSKPM GTQTHTMIFD NAFNCTFEYI SDAFSLDVSE K SGNFKHLR EFVFKNKDGF LYVYKGYQPI DVVRDLPSGF NTLKPIFKLP LGIKITNFRA ILTAFLPAQD TWGTSAAAYF VG YLKPTKF MLKYDENGTI TDAVDCSQNP LAELKCSVKS FEIDKGIYQT SNFRVVPSGD VVRFPNITNL CPFGEVFNAT KFP SVYAWE RKRISNCVAD YSVLYNSTSF STFKCYGVSA TKLNDLCFSN VYADSFVVKG DDVRQIAPGQ TGVIADYNYK LPDD FMGCV LAWNTRNIDA TSTGNYNYKY RYLRHGKLRP FERDISNVPF SPDGKPCTPP ALNCYWPLKD YGFYTTSGIG YQPYR VVVL SFELLNAPAT VCGPKLSTDL IKNQCVNFNF NGLTGTGVLT PSSKRFQPFQ QFGRDVSDFT DSVRDPKTSE ILDISP CSF GGVSVITPGT NASSEVAVLY QDVNCTDVPT AIHADQLTPA WRIYSTGNNV FQTQAGCLIG AEHVDTSYEC DIPIGAG IC ASYHTVSSLR STSQKSIVAY TMSLGADSSI AYSNNTIAIP TNFLISITTE VMPVSMAKTS VDCNMYICGD STECANLL L QYGSFCAQLN RALSGIAVEQ DRNTREVFAQ VKQMYKTPTL KDFGGFNFSQ ILPDPLKPTK RSFIEDLLFN KVTLADAGF MKQYGECLGD INARDLICAQ KFNGLTVLPP LLTDDMIAAY TAALVSGTAT AGWTFGAGAA LQIPFAMQMA YRFNGIGVAQ NVLYENQKQ IANQFNKAIS QIQESLTTTS TALGKLQDVV NQNAQALNTL VKQLSSNFGA ISSVLNDILS RLDKVEAEVQ I DRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FPQAAPHGVV FLHVTYVPSQ ER NFTTAPA ICHEGKAYFP REGVFVFNGT SWFITQRNFF SPQIITTDNT FVSGNCDVVI GIINNTVYD |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #8: LINOLEIC ACID
Macromolecule | Name: LINOLEIC ACID / type: ligand / ID: 8 / Number of copies: 3 / Formula: EIC |
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Molecular weight | Theoretical: 280.445 Da |
Chemical component information | ChemComp-EIC: |
-Macromolecule #9: water
Macromolecule | Name: water / type: ligand / ID: 9 / Number of copies: 352 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 750000 |