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- EMDB-36906: SARS-CoV-2 BA.1 spike with UT28-RD -

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Entry
Database: EMDB / ID: EMD-36906
TitleSARS-CoV-2 BA.1 spike with UT28-RD
Map data
Sample
  • Complex: SARS-CoV-2 BA.1 spike protein with UT28K-RD complex
    • Complex: SARS-CoV-2 BA.1 spike protein
      • Protein or peptide: Spike glycoprotein
    • Complex: UT28K-RD Fab
      • Protein or peptide: UT28K-RD Fab heavy chain
      • Protein or peptide: UT28K-RD Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / Antibody / Spike protein / STRUCTURAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / identical protein binding / membrane / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsChen L / Kita S / Anraku Y / Maenaka K
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101077 and JP22ama121010 Japan
Japan Agency for Medical Research and Development (AMED)JP22ae0121018 Japan
Japan Society for the Promotion of Science (JSPS)JP20K07624 and JP23H02776 Japan
Japan Agency for Medical Research and Development (AMED)JP23fa627009 Japan
Other governmentJPMJCR20H8
CitationJournal: Structure / Year: 2024
Title: Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1.
Authors: Tatsuhiko Ozawa / Yoshiki Ikeda / Liuan Chen / Rigel Suzuki / Atsushi Hoshino / Akira Noguchi / Shunsuke Kita / Yuki Anraku / Emiko Igarashi / Yumiko Saga / Noriko Inasaki / Shunta Taminishi ...Authors: Tatsuhiko Ozawa / Yoshiki Ikeda / Liuan Chen / Rigel Suzuki / Atsushi Hoshino / Akira Noguchi / Shunsuke Kita / Yuki Anraku / Emiko Igarashi / Yumiko Saga / Noriko Inasaki / Shunta Taminishi / Jiei Sasaki / Yuhei Kirita / Hideo Fukuhara / Katsumi Maenaka / Takao Hashiguchi / Takasuke Fukuhara / Kenichi Hirabayashi / Hideki Tani / Hiroyuki Kishi / Hideki Niimi /
Abstract: SARS-CoV-2 rapidly mutates and acquires resistance to neutralizing antibodies. We report an in-silico-designed antibody that restores the neutralizing activity of a neutralizing antibody. Our ...SARS-CoV-2 rapidly mutates and acquires resistance to neutralizing antibodies. We report an in-silico-designed antibody that restores the neutralizing activity of a neutralizing antibody. Our previously generated antibody, UT28K, exhibited broad neutralizing activity against mutant variants; however, its efficacy against Omicron BA.1 was compromised by the mutation. Using previously determined structural information, we designed a modified-UT28K (V T28R/N57D), UT28K-RD targeting the mutation site. In vitro and in vivo experiments demonstrated the efficacy of UT28K-RD in neutralizing Omicron BA.1. Although the experimentally determined structure partially differed from the predicted model, our study serves as a successful case of antibody design, wherein the predicted amino acid substitution enhanced the recognition of the previously elusive Omicron BA.1. We anticipate that numerous similar cases will be reported, showcasing the potential of this approach for improving protein-protein interactions. Our findings will contribute to the development of novel therapeutic strategies for highly mutable viruses, such as SARS-CoV-2.
History
DepositionJul 21, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36906.png

Downloads & links

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Map

FileDownload / File: emd_36906.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 288 pix.
= 385.92 Å		1.34 Å/pix.
x 288 pix.
= 385.92 Å		1.34 Å/pix.
x 288 pix.
= 385.92 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.119
Minimum - Maximum-0.44851553 - 1.0997921
Average (Standard dev.)-0.00037885545 (±0.026298832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 385.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36906_msk_1.map
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Half map: #1

Fileemd_36906_half_map_1.map
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Half map: #2

Fileemd_36906_half_map_2.map
Projections & Slices
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Sample components

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Entire : SARS-CoV-2 BA.1 spike protein with UT28K-RD complex

EntireName: SARS-CoV-2 BA.1 spike protein with UT28K-RD complex
Components
  • Complex: SARS-CoV-2 BA.1 spike protein with UT28K-RD complex
    • Complex: SARS-CoV-2 BA.1 spike protein
      • Protein or peptide: Spike glycoprotein
    • Complex: UT28K-RD Fab
      • Protein or peptide: UT28K-RD Fab heavy chain
      • Protein or peptide: UT28K-RD Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 BA.1 spike protein with UT28K-RD complex

SupramoleculeName: SARS-CoV-2 BA.1 spike protein with UT28K-RD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: SARS-CoV-2 BA.1 spike protein

SupramoleculeName: SARS-CoV-2 BA.1 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: UT28K-RD Fab

SupramoleculeName: UT28K-RD Fab / type: complex / ID: 3 / 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: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 133.229938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GTSSQCVNLT TRTQLPPAYT NSFTRGVYYP DKVFRSSVLH STQDLFLPFF SNVTWFHVIS GTNGTKRFDN PVLPFNDGVY FASIEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LDHKNNKSWM ESEFRVYSSA NNCTFEYVSQ P FLMDLEGK ...String:
GTSSQCVNLT TRTQLPPAYT NSFTRGVYYP DKVFRSSVLH STQDLFLPFF SNVTWFHVIS GTNGTKRFDN PVLPFNDGVY FASIEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LDHKNNKSWM ESEFRVYSSA NNCTFEYVSQ P FLMDLEGK QGNFKNLREF VFKNIDGYFK IYSKHTPIIV REPEDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PG DSSSGWT AGAAAYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQPTESIVRF PNI TNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNLAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAP GQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKVSG NYNYLYRLFR KSNLKPFERD ISTEIYQAGN KPCNGVAGFN CYFPL RSYS FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL KGTGVLTESN KKFLPFQQFG RDIADT TDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTWRV YSTGSNVFQT RAGCLIG AE YVNNSYECDI PIGAGICASY QTQTKSHGSA GSVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISVTT EILPVSMT K TSVDCTMYIC GDSTECSNLL LQYGSFCTQL KRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKYFGGFNFS QILPDPSKP SKRSPIEDLL FNKVTLADAG FIKQYGDCLG DIAARDLICA QKFKGLTVLP PLLTDEMIAQ YTSALLAGTI TSGWTFGAGP ALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST PSALGKLQDV VNHNAQALNT LVKQLSSKFG A ISSVLNDI FSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SF PQSAPHG VVFLHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFVSGNCDVV IGI VNNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ YIAS

UniProtKB: Spike glycoprotein

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Macromolecule #2: UT28K-RD Fab heavy chain

MacromoleculeName: UT28K-RD Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.100398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QMQLVQSGPE VKKPGTSVKV SCKASGFRFS ISAVQWVRQA RGQRLEWIGW IVVGSGDTNY AQKFQERVTI TRDMSTSTAY MELSSLRFE DTAVYYCAAP YCGGDCSDGF DIWGQGTMVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QMQLVQSGPE VKKPGTSVKV SCKASGFRFS ISAVQWVRQA RGQRLEWIGW IVVGSGDTNY AQKFQERVTI TRDMSTSTAY MELSSLRFE DTAVYYCAAP YCGGDCSDGF DIWGQGTMVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HTCPPCPAPE GS SGHHHHH HHHHH

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Macromolecule #3: UT28K-RD Fab light chain

MacromoleculeName: UT28K-RD Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.728674 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METPAQLLFL LLLWLPDTTG EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSG TDFTLTISRL EPEDFAVYYC QQYGNSPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String:
METPAQLLFL LLLWLPDTTG EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSG TDFTLTISRL EPEDFAVYYC QQYGNSPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 34 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4161 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1146148
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 179684
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8dzh

source_name: PDB, initial_model_type: experimental model

7x7o

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8k5h:
Structure of the SARS-CoV-2 BA.1 spike with UT28-RD

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