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- EMDB-0403: SARS-CoV complex with human neutralizing S230 antibody Fab fragme... -

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Basic information

Entry
Database: EMDB / ID: EMD-0403
TitleSARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 1)
Map data
Sample
  • Complex: SARS-CoV S complex with human neutralizing S230 antibody Fab fragment (state 1)
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: S230 heavy chain
    • Protein or peptide: S230 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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 / 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 speciesSARS coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWalls AC / Xiong X / Park YJ / Tortorici MA / Snijder S / Quispe J / Cameroni E / Gopal R / Mian D / Lanzavecchia A ...Walls AC / Xiong X / Park YJ / Tortorici MA / Snijder S / Quispe J / Cameroni E / Gopal R / Mian D / Lanzavecchia A / Zambon M / Rey FA / Corti D / 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)R01GM120553 United States
CitationJournal: Cell / Year: 2019
Title: Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion.
Authors: Alexandra C Walls / Xiaoli Xiong / Young-Jun Park / M Alejandra Tortorici / Joost Snijder / Joel Quispe / Elisabetta Cameroni / Robin Gopal / Mian Dai / Antonio Lanzavecchia / Maria Zambon / ...Authors: Alexandra C Walls / Xiaoli Xiong / Young-Jun Park / M Alejandra Tortorici / Joost Snijder / Joel Quispe / Elisabetta Cameroni / Robin Gopal / Mian Dai / Antonio Lanzavecchia / Maria Zambon / Félix A Rey / Davide Corti / David Veesler /
Abstract: Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways ...Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies. To understand the humoral immune response elicited upon natural infections with coronaviruses, we structurally characterized the SARS-CoV and MERS-CoV S glycoproteins in complex with neutralizing antibodies isolated from human survivors. Although the two antibodies studied blocked attachment to the host cell receptor, only the anti-SARS-CoV S antibody triggered fusogenic conformational changes via receptor functional mimicry. These results provide a structural framework for understanding coronavirus neutralization by human antibodies and shed light on activation of coronavirus membrane fusion, which takes place through a receptor-driven ratcheting mechanism.
History
DepositionDec 6, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseFeb 6, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.36
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.36
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nb6
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0403.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.36 / Movie #1: 0.36
Minimum - Maximum-1.2724143 - 2.6183398
Average (Standard dev.)0.0034481029 (±0.04638398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 526.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z526.080526.080526.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-16-63-38
NX/NY/NZ727975
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.2722.6180.003

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Supplemental data

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Additional map: Unsharpened map

Fileemd_0403_additional.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : SARS-CoV S complex with human neutralizing S230 antibody Fab frag...

EntireName: SARS-CoV S complex with human neutralizing S230 antibody Fab fragment (state 1)
Components
  • Complex: SARS-CoV S complex with human neutralizing S230 antibody Fab fragment (state 1)
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: S230 heavy chain
    • Protein or peptide: S230 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV S complex with human neutralizing S230 antibody Fab frag...

SupramoleculeName: SARS-CoV S complex with human neutralizing S230 antibody Fab fragment (state 1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: SARS coronavirus
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightExperimental: 572 MDa

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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: SARS coronavirus
Molecular weightTheoretical: 139.815969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTSDLDRCTT FDDVQAPNYT QHTSSMRGVY YPDEIFRSDT LYLTQDLFLP FYSNVTGFH TINHTFDNPV IPFKDGIYFA ATEKSNVVRG WVFGSTMNNK SQSVIIINNS TNVVIRACNF ELCDNPFFAV S KPMGTQTH ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTSDLDRCTT FDDVQAPNYT QHTSSMRGVY YPDEIFRSDT LYLTQDLFLP FYSNVTGFH TINHTFDNPV IPFKDGIYFA ATEKSNVVRG WVFGSTMNNK SQSVIIINNS TNVVIRACNF ELCDNPFFAV S KPMGTQTH TMIFDNAFNC TFEYISDAFS LDVSEKSGNF KHLREFVFKN KDGFLYVYKG YQPIDVVRDL PSGFNTLKPI FK LPLGINI TNFRAILTAF SPAQDTWGTS AAAYFVGYLK PTTFMLKYDE NGTITDAVDC SQNPLAELKC SVKSFEIDKG IYQ TSNFRV VPSGDVVRFP NITNLCPFGE VFNATKFPSV YAWERKKISN CVADYSVLYN STFFSTFKCY GVSATKLNDL CFSN VYADS FVVKGDDVRQ IAPGQTGVIA DYNYKLPDDF MGCVLAWNTR NIDATSTGNY NYKYRYLRHG KLRPFERDIS NVPFS PDGK PCTPPALNCY WPLNDYGFYT TTGIGYQPYR VVVLSFELLN APATVCGPKL STDLIKNQCV NFNFNGLTGT GVLTPS SKR FQPFQQFGRD VSDFTDSVRD PKTSEILDIS PCSFGGVSVI TPGTNASSEV AVLYQDVNCT DVSTAIHADQ LTPAWRI YS TGNNVFQTQA GCLIGAEHVD TSYECDIPIG AGICASYHTV SLLRSTSQKS IVAYTMSLGA DSSIAYSNNT IAIPTNFS I SITTEVMPVS MAKTSVDCNM YICGDSTECA NLLLQYGSFC TQLNRALSGI AAEQDRNTRE VFAQVKQMYK TPTLKYFGG FNFSQILPDP LKPTKRSFIE DLLFNKVTLA DAGFMKQYGE CLGDINARDL ICAQKFNGLT VLPPLLTDDM IAAYTAALVS GTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLYE NQKQIANQFN KAISQIQESL TTTSTALGKL QDVVNQNAQA L NTLVKQLS SNFGAISSVL NDILSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KR VDFCGKG YHLMSFPQAA PHGVVFLHVT YVPSQERNFT TAPAICHEGK AYFPREGVFV FNGTSWFITQ RNFFSPQIIT TDN TFVSGN CDVVIGIINN TVYDPLQPEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLID LQELG KYEQYIKGSG RENLYFQGGG GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG HHHHHHHH

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Macromolecule #2: S230 heavy chain

MacromoleculeName: S230 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.314899 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QAQLVESGGA LVQPGRSLRL SCAASGFTFR NYAMHWVRQA PATGLQWLAV ITSDGRNKFY ADSVKGRFTI SREDSKNTLY LQMDSLRGE DTAVYYCVTQ RDNSRDYFPH YFHDMDVWGQ GTTVAVSS

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Macromolecule #3: S230 light chain

MacromoleculeName: S230 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.329663 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DVVLTQSPLS LPVTLGQPAS ISCRSSQSLV YSDGDTYLNW FQQRPGQSPR RLIYQVSNRD SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQGSHW PPTFGQGTKV EIK

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 17 / 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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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 K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: PDB 5x58
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 23071

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6nb6:
SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 1)

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