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- EMDB-27177: sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-27177
Titlesd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein
Map datasd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein
Sample
  • Complex: sd1.040 Fab in complex with SARS-CoV-2 Spike 2P
    • Complex: Spike glycoproteinSpike protein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: sd1.040 Fab heavy chain, sd1.040 Fab light chain
      • Protein or peptide: sd1.040 Fab heavy chain
      • Protein or peptide: sd1.040 Fab light chain
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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: 3.7 Å
AuthorsAbernathy ME / Barnes CO
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)GT15335 United States
CitationJournal: bioRxiv / Year: 2022
Title: Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2.
Authors: Filippo Bianchini / Virginia Crivelli / Morgan E Abernathy / Concetta Guerra / Martin Palus / Jonathan Muri / Harold Marcotte / Antonio Piralla / Mattia Pedotti / Raoul De Gasparo / Luca ...Authors: Filippo Bianchini / Virginia Crivelli / Morgan E Abernathy / Concetta Guerra / Martin Palus / Jonathan Muri / Harold Marcotte / Antonio Piralla / Mattia Pedotti / Raoul De Gasparo / Luca Simonelli / Milos Matkovic / Chiara Toscano / Maira Biggiogero / Veronica Calvaruso / Pavel Svoboda / Tomás Cervantes Rincón / Tommaso Fava / Lucie Podešvová / Akanksha A Shanbhag / Andrea Celoria / Jacopo Sgrignani / Michal Stefanik / Vaclav Hönig / Veronika Pranclova / Tereza Michalcikova / Jan Prochazka / Giuditta Guerrini / Dora Mehn / Annalisa Ciabattini / Hassan Abolhassani / David Jarrossay / Mariagrazia Uguccioni / Donata Medaglini / Qiang Pan-Hammarström / Luigi Calzolai / Daniel Fernandez / Fausto Baldanti / Alessandra Franzetti-Pellanda / Christian Garzoni / Radislav Sedlacek / Daniel Ruzek / Luca Varani / Andrea Cavalli / Christopher O Barnes / Davide F Robbiani /
Abstract: Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution ...Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four , including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with , including SARS-CoV-2 variants.
ONE SENTENCE SUMMARY: Broadly cross-reactive antibodies that protect from SARS-CoV-2 variants are revealed by virus coldspot-driven discovery.
History
DepositionJun 1, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27177.png

Downloads & links

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Map

FileDownload / File: emd_27177.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein
Voxel sizeX=Y=Z: 0.8521 Å
Density
Contour LevelBy AUTHOR: 0.187
Minimum - Maximum-1.0883248 - 1.5007387
Average (Standard dev.)-4.9515864e-05 (±0.014740729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 368.1072 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein

Fileemd_27177_additional_1.map
Annotationsd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein

Fileemd_27177_half_map_1.map
Annotationsd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein

Fileemd_27177_half_map_2.map
Annotationsd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : sd1.040 Fab in complex with SARS-CoV-2 Spike 2P

EntireName: sd1.040 Fab in complex with SARS-CoV-2 Spike 2P
Components
  • Complex: sd1.040 Fab in complex with SARS-CoV-2 Spike 2P
    • Complex: Spike glycoproteinSpike protein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: sd1.040 Fab heavy chain, sd1.040 Fab light chain
      • Protein or peptide: sd1.040 Fab heavy chain
      • Protein or peptide: sd1.040 Fab light chain

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Supramolecule #1: sd1.040 Fab in complex with SARS-CoV-2 Spike 2P

SupramoleculeName: sd1.040 Fab in complex with SARS-CoV-2 Spike 2P / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 79 KDa

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Supramolecule #2: Spike glycoprotein

SupramoleculeName: Spike glycoprotein / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: sd1.040 Fab heavy chain, sd1.040 Fab light chain

SupramoleculeName: sd1.040 Fab heavy chain, sd1.040 Fab light chain / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 139.787969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPR RARSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGAALQIPFA MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STASALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDL QELGK YEQYIKWPSG RLVPRGSPGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHH

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Macromolecule #2: sd1.040 Fab heavy chain

MacromoleculeName: sd1.040 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.945762 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYTFT SFYIHWVRQA PGQGLEWMGI IDPSGGSTSY PQKFQGRVTM TRDTSTSTVY MDLSSLRSE DTAVYYCTRD GSAGDNSWFD PWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT SFYIHWVRQA PGQGLEWMGI IDPSGGSTSY PQKFQGRVTM TRDTSTSTVY MDLSSLRSE DTAVYYCTRD GSAGDNSWFD PWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSCDKTH HHHHH

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Macromolecule #3: sd1.040 Fab light chain

MacromoleculeName: sd1.040 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.346984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPDS LAVSLGERAT INCKSSRNVL YSSNNKNYLA WYQQKPGQPP KLLIYWASAR ESGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQQYYN TPYTFGQGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIVMTQSPDS LAVSLGERAT INCKSSRNVL YSSNNKNYLA WYQQKPGQPP KLLIYWASAR ESGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQQYYN TPYTFGQGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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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

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mM(HOCH2)3CNH2Tris
150.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9894 / Average exposure time: 2.88 sec. / Average electron dose: 59.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4343219
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 277530
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6vxx

chain_id: A

5aze

chain_id: H

7d0d

chain_id: L
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8d48:
sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein

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