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- EMDB-27606: Cryo-EM Structure of SARS-CoV-2 HexaPro Spike ectodomain in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-27606
TitleCryo-EM Structure of SARS-CoV-2 HexaPro Spike ectodomain in complex with DH1338 Fab, 3-RBD-up conformation
Map dataSharp map from homogeneous C1 refinement in cryosparc
Sample
  • Complex: Ab026500 Fab bound to SARS-CoV-2 HexaPro Spike Trimer
    • Other: Spike glycoprotein HexaPro
    • Other: DH1338 Fab Heavy Chain
    • Other: DH1338 Fab Light Chain
KeywordsSARS-CoV-2 / VIRAL PROTEIN / Antibody / Fab / RBD / 3-RBD-up
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsStalls V / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI165947 United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of SARS-CoV-2 HexaPro Spike ectodomain in complex with DH1338 Fab, 3-RBD-up conformation
Authors: Stalls V / Acharya P / Malewana D
History
DepositionJul 13, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27606.png

Downloads & links

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Map

FileDownload / File: emd_27606.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map from homogeneous C1 refinement in cryosparc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.697
Minimum - Maximum-3.7345433 - 7.71856
Average (Standard dev.)-0.0047704573 (±0.18323176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half B map from homogeneous C1 refinement in cryosparc

Fileemd_27606_half_map_1.map
AnnotationHalf B map from homogeneous C1 refinement in cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A map from homogeneous C1 refinement in cryosparc

Fileemd_27606_half_map_2.map
AnnotationHalf A map from homogeneous C1 refinement in cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ab026500 Fab bound to SARS-CoV-2 HexaPro Spike Trimer

EntireName: Ab026500 Fab bound to SARS-CoV-2 HexaPro Spike Trimer
Components
  • Complex: Ab026500 Fab bound to SARS-CoV-2 HexaPro Spike Trimer
    • Other: Spike glycoprotein HexaPro
    • Other: DH1338 Fab Heavy Chain
    • Other: DH1338 Fab Light Chain

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Supramolecule #1: Ab026500 Fab bound to SARS-CoV-2 HexaPro Spike Trimer

SupramoleculeName: Ab026500 Fab bound to SARS-CoV-2 HexaPro Spike Trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 556 KDa

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Macromolecule #1: Spike glycoprotein HexaPro

MacromoleculeName: Spike glycoprotein HexaPro / type: other / ID: 1 / Classification: other
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
SequenceString: VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGWI FGTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLGVYY HKNNKSWMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN ...String:
VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGWI FGTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLGVYY HKNNKSWMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN FKNLREFVFK NIDGYFKIYS KHTPINLVRD LPQGFSALEP LVDLPIGINI TRFQTLLALH RSYLTPGDSS SGWTAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPFGEVFNAT RFASVYAWNR KRISNCVADY SVLYNSASFS TFKCYGVSPT KLNDLCFTNV YADSFVIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPCNGVEG FNCYFPLQSY GFQPTNGVGY QPYRVVVLSF ELLHAPATVC GPKKSTNLVK NKCVNFNFNG LTGTGVLTES NKKFLPFQQF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQDV NCTEVPVAIH ADQLTPTWRV YSTGSNVFQT RAGCLIGAEH VNNSYECDIP IGAGICASYQ TQTNSPGSAS SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLNR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK DFGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTPSAL GKLQDVVNQN AQALNTLVKQ LSSNFGAISS VLNDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVYDPLQPEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLIDLQELGK YEQGSGYIPE APRDGQAYVR KDGEWVLLST FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAWSHPQ FEK
Recombinant expressionOrganism: Mammalia (mammals)

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Macromolecule #2: DH1338 Fab Heavy Chain

MacromoleculeName: DH1338 Fab Heavy Chain / type: other / ID: 2 / Classification: other
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
SequenceString: MGWSCIILFL VATATGVHAQ LQLQESGPGL VKPSETLSLT CAVSGGSISR KNWSWIRQPP GKGLGWIGRI SGSGGSTDYN PSLKSRVTIS TDTSKNQFSL KLSSVTAADT AVYYCARVAY YEDDYGYYYT EGAFDFWGQG LRVTVSSAST KGPSVFPLAP SSRSTSESTA ...String:
MGWSCIILFL VATATGVHAQ LQLQESGPGL VKPSETLSLT CAVSGGSISR KNWSWIRQPP GKGLGWIGRI SGSGGSTDYN PSLKSRVTIS TDTSKNQFSL KLSSVTAADT AVYYCARVAY YEDDYGYYYT EGAFDFWGQG LRVTVSSAST KGPSVFPLAP SSRSTSESTA ALGCLVKDYF PEPVTVSWNS GSLTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYVC NVNHKPSNTK VDKRVEI
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #3: DH1338 Fab Light Chain

MacromoleculeName: DH1338 Fab Light Chain / type: other / ID: 3 / Classification: other
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
SequenceString: MGWSCIILFL VATATGVHAE IVMTQSPATL SLSPGERATL SCRTSQSVSS YVAWYQQKPE QTPRLLIYDA SSRATGIPDR FSGGGSGTDF TLTISSLEPE DFAVYYCQQY SNWPWTFGQG TKVEIKRAVA APSVFIFPPS EDQVKSGTVS VVCLLNNFYP REASVKWKVD ...String:
MGWSCIILFL VATATGVHAE IVMTQSPATL SLSPGERATL SCRTSQSVSS YVAWYQQKPE QTPRLLIYDA SSRATGIPDR FSGGGSGTDF TLTISSLEPE DFAVYYCQQY SNWPWTFGQG TKVEIKRAVA APSVFIFPPS EDQVKSGTVS VVCLLNNFYP REASVKWKVD GVLKTGNSQE SVTEQDSKDN TYSLSSTLTL SSTDYQSHNV YACEVTHQGL SSPVTKSFNR GEC
Recombinant expressionOrganism: Homo sapiens (human)

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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

Concentration1.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP
DetailsFab to spike 6:1 ratio.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7865 / Average electron dose: 59.4 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: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Coot, ISOLDE, PHENIX) / Number images used: 1109951
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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