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- EMDB-25263: SARS-CoV-2 S B.1.617.2 delta variant + S2M11 + S2L20 Global Refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-25263
TitleSARS-CoV-2 S B.1.617.2 delta variant + S2M11 + S2L20 Global Refinement
Map datasharpened map
Sample
  • Complex: SARS-CoV-2 S B.1.617.2 delta variant + S2M11 Fab + S2L20 Fab
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: S2M11 Fab light chain
    • Protein or peptide: S2M11 Fab heavy chain
    • Protein or peptide: S2L20 Fab light chain
    • Protein or peptide: S2L20 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMcCallum M / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Science / Year: 2021
Title: Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
Authors: Matthew McCallum / Alexandra C Walls / Kaitlin R Sprouse / John E Bowen / Laura E Rosen / Ha V Dang / Anna De Marco / Nicholas Franko / Sasha W Tilles / Jennifer Logue / Marcos C Miranda / ...Authors: Matthew McCallum / Alexandra C Walls / Kaitlin R Sprouse / John E Bowen / Laura E Rosen / Ha V Dang / Anna De Marco / Nicholas Franko / Sasha W Tilles / Jennifer Logue / Marcos C Miranda / Margaret Ahlrichs / Lauren Carter / Gyorgy Snell / Matteo Samuele Pizzuto / Helen Y Chu / Wesley C Van Voorhis / Davide Corti / David Veesler /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission leads to the emergence of variants, including the B.1.617.2 (Delta) variant of concern that is causing a new wave of ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission leads to the emergence of variants, including the B.1.617.2 (Delta) variant of concern that is causing a new wave of infections and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing their immune evasion. Mutations in the B.1.617.1 (Kappa) and Delta spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including remodeling of the Delta amino-terminal domain. The angiotensin-converting enzyme 2 binding affinities of the Kappa and Delta receptor binding domains are comparable to the Wuhan-Hu-1 isolate, whereas B.1.617.2+ (Delta+) exhibits markedly reduced affinity.
History
DepositionOct 29, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateJan 5, 2022-
Current statusJan 5, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7so9
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25263.png

Downloads & links

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Map

FileDownload / File: emd_25263.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 0.843 Å
Density
Contour LevelBy AUTHOR: 1.2 / Movie #1: 0.5
Minimum - Maximum-6.0894966 - 9.074593
Average (Standard dev.)0.0041985908 (±0.098331995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 431.616 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8430.8430.843
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z431.616431.616431.616
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-6.0899.0750.004

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Supplemental data

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Additional map: unsharpened map

Fileemd_25263_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map a

Fileemd_25263_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_25263_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 S B.1.617.2 delta variant + S2M11 Fab + S2L20 Fab

EntireName: SARS-CoV-2 S B.1.617.2 delta variant + S2M11 Fab + S2L20 Fab
Components
  • Complex: SARS-CoV-2 S B.1.617.2 delta variant + S2M11 Fab + S2L20 Fab
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: S2M11 Fab light chain
    • Protein or peptide: S2M11 Fab heavy chain
    • Protein or peptide: S2L20 Fab light chain
    • Protein or peptide: S2L20 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: SARS-CoV-2 S B.1.617.2 delta variant + S2M11 Fab + S2L20 Fab

SupramoleculeName: SARS-CoV-2 S B.1.617.2 delta variant + S2M11 Fab + S2L20 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 141.522891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLRT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLDVYYHKNN KSWMESGVYS S ANNCTFEY ...String:
MFVFLVLLPL VSSQCVNLRT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLDVYYHKNN KSWMESGVYS S ANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LL ALHRSYL TPGDSSSGWT AGAAAYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQP TESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVI RGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYRYRLFR KSNLKPFERD ISTEIYQAGS KPCNG VEGF NCYFPLQSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL TGTGVLTESN KKFLPF QQF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTWRV YSTGSNV FQ TRAGCLIGAE HVNNSYECDI PIGAGICASY QTQTNSRRRA RSVASQSIIA YTMSLGAENS VACSNNSIAI PTNFTISV T TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL NRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKDFGGFNF SQILPDPSKP SKRSPIEDLL FNKVTLADAG FIKQYGDCLG DIAARDLICA QKFNGLTVLP PLLTDEMIAQ YTSALLAGTI CSGWTFGAG PALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST PSALGKLQNV VNQNAQALNT L VKQLSSNF GAISSVLNDI LSRLDKPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DF CGKGYHL MSFPQSAPHG VVFLHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFV SGNCDV VIGIVNNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQE LGKYE QGSGYIPEAP RDGQAYVRKD GEWVLLSTFL GRSLEVLFQG PGSGGLNDIF EAQKIEWHEG SGHHHHHHHH

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Macromolecule #2: S2M11 Fab light chain

MacromoleculeName: S2M11 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.208458 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IVMMQSPGTL SLSPGERATL SCRASQSVSS SYLAWYQQKP GQAPRLLIYG ASSRATGIPD RFSGSGSGTD FTLTISRLEP EDFAVYYCQ QYGSSAWTFG QGTKV

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Macromolecule #3: S2M11 Fab heavy chain

MacromoleculeName: S2M11 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.65122 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVQSGAEV KKPGASVKVS CKASGYTFTG YYMHWVRQAP GQGLEWMGWI NPISSGTSYA QTFQGRVTMT SDTSITTAYM ELSRLRSDD TAVYYCARAA PFYDFWSGYS YFDYWGQGTL VTV

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Macromolecule #4: S2L20 Fab light chain

MacromoleculeName: S2L20 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.829141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VIWMTQSPSS LSASVGDRVT ITCQASQDIR FYLNWYQQKP GKAPKLLISD ASNMETGVPS RFSGSGSGTD FTFTISSLQP EDIATYYCQ QYDNLPFTFG PGTKVDFK

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Macromolecule #5: S2L20 Fab heavy chain

MacromoleculeName: S2L20 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.453958 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG VVQPGGSLRL SCAASGFTFN SYGMHWVRQA PGKGLEWVAF IRYDGGNKYY ADSVKGRFTI SRDNSKNTLY LQMKSLRAE DTAVYYCANL KDSRYSGSYY DYWGQGTLVT VS

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 45 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 354 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 543668

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