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- EMDB-33975: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with... -

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Basic information

Entry
Database: EMDB / ID: EMD-33975
TitleCryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with C480A mutation
Map data
Sample
  • Complex: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with C480A mutation
    • Protein or peptide: Spike glycoprotein
KeywordsSARS-CoV-2 / spike / Antibody / IgG / Fab / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsAnzai I / Fujita J / Ono C / Kosaka Y / Miyamoto Y / Shichinohe S / Takada K / Torii S / Taguwa S / Suzuki K ...Anzai I / Fujita J / Ono C / Kosaka Y / Miyamoto Y / Shichinohe S / Takada K / Torii S / Taguwa S / Suzuki K / Makino F / Kajita T / Inoue T / Namba K / Watanabe T / Matsuura Y
Funding support Japan, 23 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16H06429 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16K21723 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16H06432 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16H06429 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16K21723 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16H06434 Japan
Japan Society for the Promotion of Science (JSPS)JP22H02521 Japan
Japan Society for the Promotion of Science (JSPS)JP21K15042 Japan
Japan Society for the Promotion of Science (JSPS)JP21H02736 Japan
Japan Society for the Promotion of Science (JSPS)JP25K000013 Japan
Japan Society for the Promotion of Science (JSPS)JP20K22630 Japan
Japan Agency for Medical Research and Development (AMED)JP20fk0108281 Japan
Japan Agency for Medical Research and Development (AMED)JP19fk0108113 Japan
Japan Agency for Medical Research and Development (AMED)JP20fk0108401 Japan
Japan Agency for Medical Research and Development (AMED)JP21fk0108493 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP20pc0101047 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Japan Science and TechnologyJPMJOP1861 Japan
Japan Science and TechnologyJPMJMS2025 Japan
JEOL YOKOGUSHI Research Alliance Laboratories of Osaka University Japan
The Tokyo Biochemical Research Foundation Japan
Takeda Science Foundation Japan
CitationJournal: To Be Published
Title: Characterization of an antibody that neutralizes a wide range of SARS-CoV-2 variants by recognizing a novel epitope in the loop region adjacent to the ACE2-binding interface with the receptor-binding domain
Authors: Anzai I / Fujita J / Ono C / Kosaka Y / Miyamoto Y / Shichinohe S / Takada K / Torii S / Taguwa S / Suzuki K / Makino F / Kajita T / Inoue T / Namba K / Watanabe T / Matsuura Y
History
DepositionAug 1, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33975.png

Downloads & links

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Map

FileDownload / File: emd_33975.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.96 Å		0.86 Å/pix.
x 360 pix.
= 309.96 Å		0.86 Å/pix.
x 360 pix.
= 309.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.861 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.02951223 - 0.062300146
Average (Standard dev.)0.000101897334 (±0.0013714391)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33975_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33975_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33975_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with...

EntireName: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with C480A mutation
Components
  • Complex: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with C480A mutation
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with...

SupramoleculeName: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with C480A mutation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPA NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQGVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEHVNNSY ECDIPIGAGI CASYQTQTNS PGSASSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GAALQIPFAM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGSH HHHHHHH

GENBANK: GENBANK: QHD43416.1

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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

Concentration0.48 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMHEPES2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid
200.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: GRAPHENE
Details: The graphene grid was chemically oxidized and modified.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1758408
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 51201
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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