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- EMDB-31017: SARS-CoV-2 NTD in complex with N9 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-31017
TitleSARS-CoV-2 NTD in complex with N9 Fab
Map data
Sample
  • Complex: SARS-CoV-2 NTD in complex with N9 Fab
    • Complex: SARS-CoV-2 NTD and RBD
      • Protein or peptide: Spike protein S1
      • Protein or peptide: Spike protein S1
    • Complex: N9, 368-2 and 604H Fab
      • Protein or peptide: N9 H
      • Protein or peptide: N9 L
      • Protein or peptide: 368-2 H
      • Protein or peptide: 368-2 L
      • Protein or peptide: 604 H
      • Protein or peptide: 604 L
KeywordsSARS-CoV-2 / complex / antibody / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 / 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 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 speciesSARS coronavirus Tor2 / Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsDu S / Xiao J
CitationJournal: Cell Res / Year: 2021
Title: Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines.
Authors: Yunlong Cao / Ayijiang Yisimayi / Yali Bai / Weijin Huang / Xiaofeng Li / Zhiying Zhang / Tianjiao Yuan / Ran An / Jing Wang / Tianhe Xiao / Shuo Du / Wenping Ma / Liyang Song / Yongzheng Li ...Authors: Yunlong Cao / Ayijiang Yisimayi / Yali Bai / Weijin Huang / Xiaofeng Li / Zhiying Zhang / Tianjiao Yuan / Ran An / Jing Wang / Tianhe Xiao / Shuo Du / Wenping Ma / Liyang Song / Yongzheng Li / Xiang Li / Weiliang Song / Jiajing Wu / Shuo Liu / Xuemei Li / Yonghong Zhang / Bin Su / Xianghua Guo / Yangyang Wei / Chuanping Gao / Nana Zhang / Yifei Zhang / Yang Dou / Xiaoyu Xu / Rui Shi / Bai Lu / Ronghua Jin / Yingmin Ma / Chengfeng Qin / Youchun Wang / Yingmei Feng / Junyu Xiao / Xiaoliang Sunney Xie /
Abstract: SARS-CoV-2 variants could induce immune escape by mutations on the receptor-binding domain (RBD) and N-terminal domain (NTD). Here we report the humoral immune response to circulating SARS-CoV-2 ...SARS-CoV-2 variants could induce immune escape by mutations on the receptor-binding domain (RBD) and N-terminal domain (NTD). Here we report the humoral immune response to circulating SARS-CoV-2 variants, such as 501Y.V2 (B.1.351), of the plasma and neutralizing antibodies (NAbs) elicited by CoronaVac (inactivated vaccine), ZF2001 (RBD-subunit vaccine) and natural infection. Among 86 potent NAbs identified by high-throughput single-cell VDJ sequencing of peripheral blood mononuclear cells from vaccinees and convalescents, near half anti-RBD NAbs showed major neutralization reductions against the K417N/E484K/N501Y mutation combination, with E484K being the dominant cause. VH3-53/VH3-66 recurrent antibodies respond differently to RBD variants, and K417N compromises the majority of neutralizing activity through reduced polar contacts with complementarity determining regions. In contrast, the 242-244 deletion (242-244Δ) would abolish most neutralization activity of anti-NTD NAbs by interrupting the conformation of NTD antigenic supersite, indicating a much less diversity of anti-NTD NAbs than anti-RBD NAbs. Plasma of convalescents and CoronaVac vaccinees displayed comparable neutralization reductions against pseudo- and authentic 501Y.V2 variants, mainly caused by E484K/N501Y and 242-244Δ, with the effects being additive. Importantly, RBD-subunit vaccinees exhibit markedly higher tolerance to 501Y.V2 than convalescents, since the elicited anti-RBD NAbs display a high diversity and are unaffected by NTD mutations. Moreover, an extended gap between the third and second doses of ZF2001 leads to better neutralizing activity and tolerance to 501Y.V2 than the standard three-dose administration. Together, these results suggest that the deployment of RBD-vaccines, through a third-dose boost, may be ideal for combating SARS-CoV-2 variants when necessary, especially for those carrying mutations that disrupt the NTD supersite.
History
DepositionMar 1, 2021-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0359
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0359
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7e8f
  • Surface level: 0.0359
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7e8f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31017.png

Downloads & links

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Map

FileDownload / File: emd_31017.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 160 pix.
= 168.32 Å		1.05 Å/pix.
x 160 pix.
= 168.32 Å		1.05 Å/pix.
x 160 pix.
= 168.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0359 / Movie #1: 0.0359
Minimum - Maximum-0.11781918 - 0.19480054
Average (Standard dev.)0.0011533451 (±0.008974845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 168.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0521.0521.052
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z168.320168.320168.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-288-288-288
NX/NY/NZ576576576
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1180.1950.001

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Supplemental data

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Mask #1

Fileemd_31017_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_31017_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_31017_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 NTD in complex with N9 Fab

EntireName: SARS-CoV-2 NTD in complex with N9 Fab
Components
  • Complex: SARS-CoV-2 NTD in complex with N9 Fab
    • Complex: SARS-CoV-2 NTD and RBD
      • Protein or peptide: Spike protein S1
      • Protein or peptide: Spike protein S1
    • Complex: N9, 368-2 and 604H Fab
      • Protein or peptide: N9 H
      • Protein or peptide: N9 L
      • Protein or peptide: 368-2 H
      • Protein or peptide: 368-2 L
      • Protein or peptide: 604 H
      • Protein or peptide: 604 L

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Supramolecule #1: SARS-CoV-2 NTD in complex with N9 Fab

SupramoleculeName: SARS-CoV-2 NTD in complex with N9 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: SARS coronavirus Tor2

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Supramolecule #2: SARS-CoV-2 NTD and RBD

SupramoleculeName: SARS-CoV-2 NTD and RBD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #8
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: N9, 368-2 and 604H Fab

SupramoleculeName: N9, 368-2 and 604H Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#7

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 33.040246 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SQCVNLTTRT QLPPAYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDNP VLPFNDGVYF ASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV S QPFLMDLE ...String:
SQCVNLTTRT QLPPAYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDNP VLPFNDGVYF ASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV S QPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PG DSSSGWT AGAAAYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTL

UniProtKB: Spike glycoprotein

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Macromolecule #2: N9 H

MacromoleculeName: N9 H / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.300135 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVKPGGSLRL SCAASEFTFS SYSMNWVRQA PGKGLEWVSS ISSSGSQIYY ADSVKGRFTI SRDNAKKSLY LQMNSLRVE DTAVYYCATN GGAHSSTWSF YGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
EVQLVESGGG LVKPGGSLRL SCAASEFTFS SYSMNWVRQA PGKGLEWVSS ISSSGSQIYY ADSVKGRFTI SRDNAKKSLY LQMNSLRVE DTAVYYCATN GGAHSSTWSF YGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC DK

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Macromolecule #3: N9 L

MacromoleculeName: N9 L / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.525889 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYELTQPPSV SVSPGQTATI TCSGDKLGDK YACWYQQRPG QSPVLVIYQD SKRPSGIPER FSGSNSGNTA TLTIGGTQAM DEAAYFCQA WDSNTGVFGG GTKLTVLSQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS ...String:
SYELTQPPSV SVSPGQTATI TCSGDKLGDK YACWYQQRPG QSPVLVIYQD SKRPSGIPER FSGSNSGNTA TLTIGGTQAM DEAAYFCQA WDSNTGVFGG GTKLTVLSQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS NNKYAASSYL SLTPEQWKSH RSYSCQVTHE GSTVEKTVAP TECS

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Macromolecule #4: 368-2 H

MacromoleculeName: 368-2 H / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.355225 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGG VVQPGGSLRL SCAASGFAFT TYAMNWVRQA PGRGLEWVSA ISDGGGSAYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKT RGRGLYDYVW GSKDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
EVQLLESGGG VVQPGGSLRL SCAASGFAFT TYAMNWVRQA PGRGLEWVSA ISDGGGSAYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKT RGRGLYDYVW GSKDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC DK

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Macromolecule #5: 368-2 L

MacromoleculeName: 368-2 L / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.901645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL HSNGYLYLDW YLQKPGQSPQ LLIYLGSNRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PGTFGQGTRL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL HSNGYLYLDW YLQKPGQSPQ LLIYLGSNRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PGTFGQGTRL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #6: 604 H

MacromoleculeName: 604 H / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.367301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LIQPGGSLRL SCAASGIIVS SNYMTWVRQA PGKGLEWVSV IYSGGSTFYA DSVKGRFTIS RDKSKNTLYL QMSSLRAED TAVYYCARDL GPYGMDVWGQ GTTVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
EVQLVESGGG LIQPGGSLRL SCAASGIIVS SNYMTWVRQA PGKGLEWVSV IYSGGSTFYA DSVKGRFTIS RDKSKNTLYL QMSSLRAED TAVYYCARDL GPYGMDVWGQ GTTVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDK

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Macromolecule #7: 604 L

MacromoleculeName: 604 L / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.290756 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLTQSPSF LSASVGDRVT ITCRASQGIS SDLAWYQQKP GKAPNLLIYA ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QLNSDLYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQLTQSPSF LSASVGDRVT ITCRASQGIS SDLAWYQQKP GKAPNLLIYA ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QLNSDLYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #8: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 25.122336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF ...String:
RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF NCYFPLQSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNF

UniProtKB: Spike glycoprotein

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 63.27 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 304696
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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