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- EMDB-25209: Structure of human SARS-CoV-2 neutralizing antibody C1C-A3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-25209
TitleStructure of human SARS-CoV-2 neutralizing antibody C1C-A3 Fab
Map data
Sample
  • Complex: SARS-CoV-2_Hexapro in complex with neutralizing antibody C1C-A3 Fab from human patient
    • Complex: SARS-CoV-2 spike protein SARS-CoV-2 Hexapro
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: C1C-A3 Fab
      • Protein or peptide: neutralizing antibody C1C-A3 Fab heavy chain
      • Protein or peptide: neutralizing antibody C1C-A3 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 / 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 / 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: 4.3 Å
AuthorsPan J / Abraham J / Yang P / Shankar S
Funding support United States, 1 items
OrganizationGrant numberCountry
Other privateno grant number United States
CitationJournal: Science / Year: 2022
Title: Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.
Authors: Katherine G Nabel / Sarah A Clark / Sundaresh Shankar / Junhua Pan / Lars E Clark / Pan Yang / Adrian Coscia / Lindsay G A McKay / Haley H Varnum / Vesna Brusic / Nicole V Tolan / Guohai ...Authors: Katherine G Nabel / Sarah A Clark / Sundaresh Shankar / Junhua Pan / Lars E Clark / Pan Yang / Adrian Coscia / Lindsay G A McKay / Haley H Varnum / Vesna Brusic / Nicole V Tolan / Guohai Zhou / Michaël Desjardins / Sarah E Turbett / Sanjat Kanjilal / Amy C Sherman / Anand Dighe / Regina C LaRocque / Edward T Ryan / Casey Tylek / Joel F Cohen-Solal / Anhdao T Darcy / Davide Tavella / Anca Clabbers / Yao Fan / Anthony Griffiths / Ivan R Correia / Jane Seagal / Lindsey R Baden / Richelle C Charles / Jonathan Abraham /
Abstract: Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we ...Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.
History
DepositionOct 27, 2021-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateFeb 2, 2022-
Current statusFeb 2, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0075
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0075
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sn2
  • Surface level: 0.0075
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7sn2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25209.png

Downloads & links

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Map

FileDownload / File: emd_25209.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.0075 / Movie #1: 0.0075
Minimum - Maximum-0.024727501 - 0.03842418
Average (Standard dev.)1.7668124e-05 (±0.0017216045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 198.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8250.8250.825
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z198.000198.000198.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0250.0380.000

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Supplemental data

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Sample components

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Entire : SARS-CoV-2_Hexapro in complex with neutralizing antibody C1C-A3 F...

EntireName: SARS-CoV-2_Hexapro in complex with neutralizing antibody C1C-A3 Fab from human patient
Components
  • Complex: SARS-CoV-2_Hexapro in complex with neutralizing antibody C1C-A3 Fab from human patient
    • Complex: SARS-CoV-2 spike protein SARS-CoV-2 Hexapro
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: C1C-A3 Fab
      • Protein or peptide: neutralizing antibody C1C-A3 Fab heavy chain
      • Protein or peptide: neutralizing antibody C1C-A3 Fab light chain

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Supramolecule #1: SARS-CoV-2_Hexapro in complex with neutralizing antibody C1C-A3 F...

SupramoleculeName: SARS-CoV-2_Hexapro in complex with neutralizing antibody C1C-A3 Fab from human patient
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: concentration of the SARS-CoV-2 spike protein SARS-CoV-2 Hexapro (trimeric) and human patient antibody C1C-A3 Fab is 0.6 and 0.3 mg/mL in the final complex sample in buffer consisting of 150 ...Details: concentration of the SARS-CoV-2 spike protein SARS-CoV-2 Hexapro (trimeric) and human patient antibody C1C-A3 Fab is 0.6 and 0.3 mg/mL in the final complex sample in buffer consisting of 150 mM NaCl and 25 mM Tris-HCl, pH 7.5. structure deposited here is one receptor binding domain (RBD) in complex with on C1C-A3 Fab determined from the relate wwPDB deposit D_1000258559.
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: isolate Wuhan-Hu-1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK-293 (Thermo Fisher Expi293F) / Recombinant plasmid: pHLSec
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: SARS-CoV-2 spike protein SARS-CoV-2 Hexapro

SupramoleculeName: SARS-CoV-2 spike protein SARS-CoV-2 Hexapro / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: isolate Wuhan-Hu-1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK-293 (Thermo Fisher Expi293F) / Recombinant plasmid: pHLSec

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Supramolecule #3: C1C-A3 Fab

SupramoleculeName: C1C-A3 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Details: Fab of C1C-A3 antibody recombinantly expressed using sequence sequenced from single B cells from human patient peripheral blood sample
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK-293 (Thermo Fisher Expi293F) / Recombinant plasmid: pVRC8400

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1
Details: Severe acute respiratory syndrome coronavirus 2 surface glycoprotein (residues 1-1208) of GeneBank locus QHD43416.1 (amino acids 1-15 are the endogenous signal peptide, 16-1208 are SARS-CoV- ...Details: Severe acute respiratory syndrome coronavirus 2 surface glycoprotein (residues 1-1208) of GeneBank locus QHD43416.1 (amino acids 1-15 are the endogenous signal peptide, 16-1208 are SARS-CoV-2 spike protein residues 16-1208, 1209-1210+1237-1239+1255-1258 are linkers, 1211-1236 are T4 fibritinn foldon, 1240-1254 are the avi-tag for biotinylation, 1259-1265 are the TEV protease cleavage site, 1266-1273 are the 8xHis tag; mutations include R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 141.192203 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 SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGPALQIPFP MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STPSALGKLQ 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 YEQSGYIPEA PRDGQAYVRK DGEWVLLSTF LSAGGLNDIF EAQKIEWHEG ASGENLYFQG HHHHHHHH

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Macromolecule #2: neutralizing antibody C1C-A3 Fab heavy chain

MacromoleculeName: neutralizing antibody C1C-A3 Fab heavy chain / type: protein_or_peptide / ID: 2
Details: amino acids 1-20 are the human tPA signal peptide, 21-22 are a linker, 23-250 are the C1C-A3 Fab heavy chain residues 1-213 (note insertions in CDR loops; numbering should be according to the PDB file).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.022607 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRGLCCVLL LCGAVFVSPS ASQVQLVESG GGVVQPGRSL RLSCAASGFT FSSYGMHWVR QAPGKGLEWV AVIWYDGTNT YYADSVKGR FTISRDNSKN TLYLQMNSLR AEDTAVYYCA RDLAYRDYVW RYFDLWGRGT LVTVSGASTK GPSVFPLAPS S KSTSGGTA ...String:
MKRGLCCVLL LCGAVFVSPS ASQVQLVESG GGVVQPGRSL RLSCAASGFT FSSYGMHWVR QAPGKGLEWV AVIWYDGTNT YYADSVKGR FTISRDNSKN TLYLQMNSLR AEDTAVYYCA RDLAYRDYVW RYFDLWGRGT LVTVSGASTK GPSVFPLAPS S KSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VD KRVEPKS CDR

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Macromolecule #3: neutralizing antibody C1C-A3 Fab light chain

MacromoleculeName: neutralizing antibody C1C-A3 Fab light chain / type: protein_or_peptide / ID: 3
Details: amino acids 1-20 are the human tPA signal peptide, 21-22 are a linker, 23-238 are the C1C-A3 Fab light chain residues 1-212 (note insertions in CDR loops; numbering should be according to the PDB file).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.896107 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRGLCCVLL LCGAVFVSPS ASEIVLTQSP ATLSLSPGER ATLSCRASQS VSTYLAWYQQ KFGQAPRLLI YDASNRATGI PARFSGSGS GTDFTLTISS LEPEDFAVYY CQCRSNWPPG ITFGQGTRLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL L NNFYPREA ...String:
MKRGLCCVLL LCGAVFVSPS ASEIVLTQSP ATLSLSPGER ATLSCRASQS VSTYLAWYQQ KFGQAPRLLI YDASNRATGI PARFSGSGS GTDFTLTISS LEPEDFAVYY CQCRSNWPPG ITFGQGTRLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL L NNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

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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

Concentration0.9 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mmol/LC4H11NO3Tris
150.0 mmol/LNaClSodium chloridesodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
Details: Quantifoil Cu 1.2/1.3 2nm carbon 300 mesh grids glowed discharge at 15 mA in Pelco EasiGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4-6 seconds.
Detailsthis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 60606 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K / Max: 77.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 4583 / Average exposure time: 1.9 sec. / Average electron dose: 56.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1296929
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1.2)
Final 3D classificationNumber classes: 5 / Avg.num./class: 101973 / Software - Name: cryoSPARC (ver. 2.14.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14.2) / Number images used: 344920

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