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- EMDB-16028: Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-16028
TitleCryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 (map 4, one RBD up)
Map datasharpened map
Sample
  • Complex: SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25
    • Protein or peptide: SARS-CoV-2 spike protein (Omicron BA.1 variant)
    • Protein or peptide: Nanobody W25
KeywordsSARS-CoV-2 / spike / Omicron / BA.1 / nanobody / W25 / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.97 Å
AuthorsModhiran N / Lauer S / Spahn CMT / Watterson D / Schwefel D
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHW1851/1-2 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 (map 4, one RBD up)
Authors: Schwefel D
History
DepositionOct 27, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16028.png

Downloads & links

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Map

FileDownload / File: emd_16028.map.gz / Format: CCP4 / Size: 51.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 238 pix.
= 357. Å		1.5 Å/pix.
x 238 pix.
= 357. Å		1.5 Å/pix.
x 238 pix.
= 357. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.49016473 - 1.6704094
Average (Standard dev.)0.0011460189 (±0.064967155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions238238238
Spacing238238238
CellA=B=C: 357.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16028_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_16028_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_16028_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25

EntireName: SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25
Components
  • Complex: SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25
    • Protein or peptide: SARS-CoV-2 spike protein (Omicron BA.1 variant)
    • Protein or peptide: Nanobody W25

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Supramolecule #1: SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25

SupramoleculeName: SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: SARS-CoV-2 spike protein (Omicron BA.1 variant)

MacromoleculeName: SARS-CoV-2 spike protein (Omicron BA.1 variant) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL D HKNNKSWM ESEFRVYSSA NNCTFEYVSQ ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL D HKNNKSWM ESEFRVYSSA NNCTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPIIVR EP EDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENG TITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQPTESIVRF PNITNLCPFD EVFNATRFAS VYAW NRKRI SNCVADYSVL YNLAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGNI ADYNY KLPD DFTGCVIAWN SNKLDSKVSG NYNYLYRLFR KSNLKPFERD ISTEIYQAGN KPCNGVAGFN CYFPLR SYS FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL KGTGVLTESN KKFLPFQ QF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTW R VYSTGSNVFQ TRAGCLIGAE YVNNSYECDI PIGAGICASY QTQTKSHRRA RSVASQSIIA YTMSLGAEN SVAYSNNSIA IPTNFTISVT TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL KRALTGIAVE QDKNTQEVF AQVKQIYKTP PIKYFGGFNF SQILPDPSKP SKRSFIEDLL FNKVTLADAG FIKQYGDCLG D IAARDLIC AQKFKGLTVL PPLLTDEMIA QYTSALLAGT ITSGWTFGAG AALQIPFAMQ MAYRFNGIGV TQ NVLYENQ KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNHNAQALN TLVKQLSSKF GAISSVLNDI FSR LDKVEA EVQIDRLITG RLQSLQTYVT QQLIRAAEIR ASANLAATKM SECVLGQSKR VDFCGKGYHL MSFP QSAPH GVVFLHVTYV PAQEKNFTTA PAICHDGKAH FPREGVFVSN GTHWFVTQRN FYEPQIITTD NTFVS GNCD VVIGIVNNTV YDPLQPELDS FKEELDKYFK NHTSPDVDLG DISGINASVV NIQKEIDRLN EVAKNL NES LIDLQELGKY EQYIKWPWYI WLGFIAGLIA IVMVTIMLCC MTSCCSCLKG CCSCGSCCKF DEDDSEP VL KGVKLHYT

GENBANK: GENBANK: UFO69279.1

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Macromolecule #2: Nanobody W25

MacromoleculeName: Nanobody W25 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYLLPTAAA GLLLLAAQP A MAQVQLVE SG GGLVQPG ESL RLSCAA SGSI FGIYA VHWFR MAPG KEREFT AGF GSHGSTN YA ASVKGRFT M SRDNAKNTT YLQMNSLKPA DTAVYYCHA L IKNELGFL DY WGPGTQV TVS SAAAHH HHHH GAAEQ KLISE EDLN GAA

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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

Concentration0.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
10.0 mMTris-HCltris-(hydroxymethyl)-aminomethan -hydrochlorid
150.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9125 / Average exposure time: 3.3 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000

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Image processing

Particle selectionNumber selected: 2458527
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 32512
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.3.1)

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