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- EMDB-31624: Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike gly... -

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Basic information

Entry
Database: EMDB / ID: EMD-31624
TitleCryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex with two T6 Fab
Map data
Sample
  • Complex: S protein of South African (B.1.351) SARS-CoV-2 spike in complex with T6 Fab
    • Complex: S protein of South African (B.1.351) SARS-CoV-2
      • Protein or peptide: Spike glycoprotein,Envelope glycoprotein
    • Complex: T6 Fab
      • Protein or peptide: T6 heavy chain
      • Protein or peptide: T6 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / 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
Fibritin C-terminal / Fibritin C-terminal region / 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 ...Fibritin C-terminal / Fibritin C-terminal region / 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
Envelope glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsWang X / Zhang L / Zhang S / Liang Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: iScience / Year: 2022
Title: RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants.
Authors: Qingtai Liang / Yifeng Wang / Shuyuan Zhang / Jing Sun / Wenbo Sun / Jizhou Li / Yaping Liu / Mingxi Li / Lin Cheng / Yuhang Jiang / Ruoke Wang / Rui Zhang / Zihan Yang / Yifei Ren / Peng ...Authors: Qingtai Liang / Yifeng Wang / Shuyuan Zhang / Jing Sun / Wenbo Sun / Jizhou Li / Yaping Liu / Mingxi Li / Lin Cheng / Yuhang Jiang / Ruoke Wang / Rui Zhang / Zihan Yang / Yifei Ren / Peng Chen / Peng Gao / Huayuan Yan / Zheng Zhang / Qi Zhang / Xuanling Shi / Jianbin Wang / Wanli Liu / Xinquan Wang / Bo Ying / Jincun Zhao / Hai Qi / Linqi Zhang /
Abstract: With the rapid emergence and spread of SARS-CoV-2 variants, development of vaccines with broad and potent protectivity has become a global priority. Here, we designed a lipid nanoparticle- ...With the rapid emergence and spread of SARS-CoV-2 variants, development of vaccines with broad and potent protectivity has become a global priority. Here, we designed a lipid nanoparticle-encapsulated, nucleoside-unmodified mRNA (mRNA-LNP) vaccine encoding the trimerized receptor-binding domain (RBD trimer) and showed its robust capability in inducing broad and protective immune responses against wild-type and major variants of concern (VOCs) in the mouse model of SARS-CoV-2 infection. The protectivity was correlated with RBD-specific B cell responses especially the long-lived plasma B cells in bone marrow, strong ability in triggering BCR clustering, and downstream signaling. Monoclonal antibodies isolated from vaccinated animals demonstrated broad and potent neutralizing activity against VOCs tested. Structure analysis of one representative antibody identified a novel epitope with a high degree of conservation among different variants. Collectively, these results demonstrate that the RBD trimer mRNA vaccine serves as a promising vaccine candidate against SARS-CoV-2 variants and beyond.
History
DepositionAug 4, 2021-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateApr 27, 2022-
Current statusApr 27, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31624.png

Downloads & links

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Map

FileDownload / File: emd_31624.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0979 Å
Density
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.01808929 - 0.058304593
Average (Standard dev.)0.00020347942 (±0.0016272364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 351.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : S protein of South African (B.1.351) SARS-CoV-2 spike in complex ...

EntireName: S protein of South African (B.1.351) SARS-CoV-2 spike in complex with T6 Fab
Components
  • Complex: S protein of South African (B.1.351) SARS-CoV-2 spike in complex with T6 Fab
    • Complex: S protein of South African (B.1.351) SARS-CoV-2
      • Protein or peptide: Spike glycoprotein,Envelope glycoprotein
    • Complex: T6 Fab
      • Protein or peptide: T6 heavy chain
      • Protein or peptide: T6 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: S protein of South African (B.1.351) SARS-CoV-2 spike in complex ...

SupramoleculeName: S protein of South African (B.1.351) SARS-CoV-2 spike in complex with T6 Fab
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: S protein of South African (B.1.351) SARS-CoV-2

SupramoleculeName: S protein of South African (B.1.351) SARS-CoV-2 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: T6 Fab

SupramoleculeName: T6 Fab / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Macromolecule #1: Spike glycoprotein,Envelope glycoprotein

MacromoleculeName: Spike glycoprotein,Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 141.515062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VNFTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFANPVLP FNDGVYFAST EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP F LMDLEGKQ ...String:
VNFTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFANPVLP FNDGVYFAST EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP F LMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPINLV RGLPQGFSAL EPLVDLPIGI NITRFQTLHR SYLTPGDSSS GW TAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKT FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPF GEVFNA TRFASVYAWN RKRISNCVAD YSVLYNSASF STFKCYGVSP TKLNDLCFTN VYADSFVIRG DEVRQIAPGQ TGNI ADYNY KLPDDFTGCV IAWNSNNLDS KVGGNYNYLY RLFRKSNLKP FERDISTEIY QAGSTPCNGV KGFNCYFPLQ SYGFQ PTYG VGYQPYRVVV LSFELLHAPA TVCGPKKSTN LVKNKCVNFN FNGLTGTGVL TESNKKFLPF QQFGRDIADT TDAVRD PQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQGVNCTEVP VAIHADQLTP TWRVYSTGSN VFQTRAGCLI GAEHVNN SY ECDIPIGAGI CASYQTQTNS PGSASSVASQ SIIAYTMSLG VENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDC T MYICGDSTEC SNLLLQYGSF CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKDFGG FNFSQILPDP SKPSKRSFI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGAALQIPF AMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL N DILSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQSA PH GVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVY DPLQPE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQGSGYIP EAPR DGQAY VRKDGEWVLL STFLGRSLEV LFQGPGHHHH HHHHSAWSHP QFEKGGGSGG GGSGGSAWSH PQFEKGSDYK DDDDK

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Macromolecule #2: T6 heavy chain

MacromoleculeName: T6 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.833083 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQQPGTE LVNPGASLKM SCKTSGYRFT SYIIHWVKQT PGQGLEWIGA IFPENDDTSY SQKFKGKATL TTDTSSSTAY MQLSSLTSE DSAVYYCARD GENVLDYWGQ GTSVTVSS

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Macromolecule #3: T6 light chain

MacromoleculeName: T6 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.572053 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QIVLTQSPSS LAVSVGEKVT LSCKSSQSLL YSNNQKNYLA WYQQKSGRSP KLLLHWTSTR ESGVPDRFTG SGSGTDFTLT ISSVKAEDL AVYYCQQYYT YPWTFGGGTK LEIK

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 25 / 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

Concentration2.2 mg/mL
BufferpH: 7.2
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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vxx

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 286245

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