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- EMDB-20527: MERS S0 trimer in complex with antibody G2 -

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Basic information

Entry
Database: EMDB / ID: EMD-20527
TitleMERS S0 trimer in complex with antibody G2
Map dataMERS S0 trimer in complex with variable domain of antibody G2
Sample
  • Complex: MERS S0 ectodomain trimer in complex with antibody G2
    • Complex: MERS S0 ectodomain trimer
      • Protein or peptide: S proteinCoronavirus spike protein
      • Protein or peptide: S proteinCoronavirus spike protein
    • Complex: antibody G2
      • Protein or peptide: G2 heavy chain
      • Protein or peptide: G2 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / 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 / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...: / endocytosis involved in viral entry into host cell / 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 / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
: / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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
Spike glycoprotein / Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsBowman CA / Pallesen J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127521 United States
CitationJournal: Cell Rep / Year: 2019
Title: Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD.
Authors: Nianshuang Wang / Osnat Rosen / Lingshu Wang / Hannah L Turner / Laura J Stevens / Kizzmekia S Corbett / Charles A Bowman / Jesper Pallesen / Wei Shi / Yi Zhang / Kwanyee Leung / Robert N ...Authors: Nianshuang Wang / Osnat Rosen / Lingshu Wang / Hannah L Turner / Laura J Stevens / Kizzmekia S Corbett / Charles A Bowman / Jesper Pallesen / Wei Shi / Yi Zhang / Kwanyee Leung / Robert N Kirchdoerfer / Michelle M Becker / Mark R Denison / James D Chappell / Andrew B Ward / Barney S Graham / Jason S McLellan /
Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the ...Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the receptor-binding domain (RBD) on MERS-CoV spike (S) protein have been characterized, but much less is known about antibodies targeting non-RBD epitopes. Here, we report the structural and functional characterization of G2, a neutralizing antibody targeting the MERS-CoV S1 N-terminal domain (S1-NTD). Structures of G2 alone and in complex with the MERS-CoV S1-NTD define a site of vulnerability comprising two loops, each of which contain a residue mutated in G2-escape variants. Cell-surface binding studies and in vitro competition experiments demonstrate that G2 strongly disrupts the attachment of MERS-CoV S to its receptor, dipeptidyl peptidase-4 (DPP4), with the inhibition requiring the native trimeric S conformation. These results advance our understanding of antibody-mediated neutralization of coronaviruses and should facilitate the development of immunotherapeutics and vaccines against MERS-CoV.
History
DepositionJul 31, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseOct 9, 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: 0.264
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.264
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pz8
  • Surface level: 0.264
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6pz8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20527.png

Downloads & links

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Map

FileDownload / File: emd_20527.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMERS S0 trimer in complex with variable domain of antibody G2
Voxel sizeX=Y=Z: 1.02 Å
Density
Contour LevelBy AUTHOR: 0.264 / Movie #1: 0.264
Minimum - Maximum-0.82995546 - 1.4599104
Average (Standard dev.)0.00041269267 (±0.06330723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 357.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z357.000357.000357.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.8301.4600.000

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Supplemental data

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Mask #1

Fileemd_20527_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map #1

Fileemd_20527_half_map_1.map
AnnotationHalf Map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map #2

Fileemd_20527_half_map_2.map
AnnotationHalf Map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MERS S0 ectodomain trimer in complex with antibody G2

EntireName: MERS S0 ectodomain trimer in complex with antibody G2
Components
  • Complex: MERS S0 ectodomain trimer in complex with antibody G2
    • Complex: MERS S0 ectodomain trimer
      • Protein or peptide: S proteinCoronavirus spike protein
      • Protein or peptide: S proteinCoronavirus spike protein
    • Complex: antibody G2
      • Protein or peptide: G2 heavy chain
      • Protein or peptide: G2 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: MERS S0 ectodomain trimer in complex with antibody G2

SupramoleculeName: MERS S0 ectodomain trimer in complex with antibody G2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: MERS S0 ectodomain trimer

SupramoleculeName: MERS S0 ectodomain trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: antibody G2

SupramoleculeName: antibody G2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: S protein

MacromoleculeName: S protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 51.301617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SVPGEMRLAS IAFNHPIQVD QLNSSYFKLS IPTNFSFGVT QEYIQTTIQK VTVDCKQYVC NGFQKCEQLL REYGQFCSKI NQALHGANL RQDDSVRNLF ASVKSSQSSP IIPGFGGDFN LTLLEPVSIS TGSRSARSAI EDLLFDKVTI ADPGYMQGYD D CMQQGPAS ...String:
SVPGEMRLAS IAFNHPIQVD QLNSSYFKLS IPTNFSFGVT QEYIQTTIQK VTVDCKQYVC NGFQKCEQLL REYGQFCSKI NQALHGANL RQDDSVRNLF ASVKSSQSSP IIPGFGGDFN LTLLEPVSIS TGSRSARSAI EDLLFDKVTI ADPGYMQGYD D CMQQGPAS ARDLICAQYV AGYKVLPPLM DVNMEAAYTS SLLGSIAGVG WTAGLSSFAA IPFAQSIFYR LNGVGITQQV LS ENQKLIA NKFNQALGAM QTGFTTTNEA FHKVQDAVNN NAQALSKLAS ELSNTFGAIS ASIGDIIQRL DVLEQDAQID RLI NGRLTT LNAFVAQQLV RSESAALSAQ LAKDKVNECV KAQSKRSGFC GQGTHIVSFV VNAPNGLYFM HVGYYPSNHI EVVS AYGLC DAANPTNCIA PVNGYFIKTN NTRIVDEWSY TGSSFYAPEP ITSLNTKYVA PQVTYQNIST NLPPPLL

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Macromolecule #2: S protein

MacromoleculeName: S protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 80.409109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF SDGKMGRFFN HTLVLLPDGC G TLLRAFYC ...String:
YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF SDGKMGRFFN HTLVLLPDGC G TLLRAFYC ILEPRSGNHC PAGNSYTSFA TYHTPATDCS DGNYNRNASL NSFKEYFNLR NCTFMYTYNI TEDEILEWFG IT QTAQGVH LFSSRYVDLY GGNMFQFATL PVYDTIKYYS IIPHSIRSIQ SDRKAWAAFY VYKLQPLTFL LDFSVDGYIR RAI DCGFND LSQLHCSYES FDVESGVYSV SSFEAKPSGS VVEQAEGVEC DFSPLLSGTP PQVYNFKRLV FTNCNYNLTK LLSL FSVND FTCSQISPAA IASNCYSSLI LDYFSYPLSM KSDLSVSSAG PISQFNYKQS FSNPTCLILA TVPHNLTTIT KPLKY SYIN KCSRLLSDDR TEVPQLVNAN QYSPCVSIVP STVWEDGDYY RKQLSPLEGG GWLVASGSTV AMTEQLQMGF GITVQY GTD TNSVCPKLEF ANDTKIASQL GNCVEYSLYG VSGRGVFQNC TAVGVRQQRF VYDAYQNLVG YYSDDGNYYC LRACVSV PV SVIYDKETKT HATLFGSVAC EHISSTMSQY SRSTRSMLKR RDSTYGPLQT PVGCVLGLVN SSLFVEDCKL PLGQSLCA L PDTPS

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Macromolecule #3: G2 heavy chain

MacromoleculeName: G2 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.275059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQSGGE LVKPGASVKL SCKTSGFTFS SSYISWLKQK PGQSLEWIAW IYAGTGGTEY NQKFTGKAQV TVDTSSSTAY MQFSSLTTE DSAIYYCARG GSSFAMDYWG QGTSVTVSSA STTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV ...String:
QVQLQQSGGE LVKPGASVKL SCKTSGFTFS SSYISWLKQK PGQSLEWIAW IYAGTGGTEY NQKFTGKAQV TVDTSSSTAY MQFSSLTTE DSAIYYCARG GSSFAMDYWG QGTSVTVSSA STTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV HTFPAVLQSD LYTLSSSVTV PSSTWPSETV TCNVAHPASS TKVDKKIVPR DCGKGLEVLF Q

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Macromolecule #4: G2 light chain

MacromoleculeName: G2 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.861293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLVLTQSPAS LAVSLGQRAT ISCRASESVD NYGISFMNWF QQKPGQPPKL LIHTASNQGS GVPARFSGSG SGTDFSLNIH PVEDDDTAM YFCQQSEEVP LTFGAGTKLE IKRTDAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String:
QLVLTQSPAS LAVSLGQRAT ISCRASESVD NYGISFMNWF QQKPGQPPKL LIHTASNQGS GVPARFSGSG SGTDFSLNIH PVEDDDTAM YFCQQSEEVP LTFGAGTKLE IKRTDAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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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: 18 / 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: 7.4
GridDetails: unspecified
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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 77.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 418781
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER / Details: Ab Initio Model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.5) / Number images used: 12386
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5w9i

DetailsModel was not refined.
Output model

PDB-6pz8:
MERS S0 trimer in complex with variable domain of antibody G2

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