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- EMDB-62591: Cryo-EM structure of SARS-CoV-2 prototype spike protein in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-62591
TitleCryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1
Map data
Sample
  • Complex: SARS-CoV-2 protoype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1
    • Complex: SARS-CoV-2 prototype spike protein
      • Protein or peptide: Spike protein S1
    • Complex: The fragments of triple-nAb 4H1, 4A5 and 4C1
      • Protein or peptide: The heavy chain of 4C1
      • Protein or peptide: The light chain of 4C1
      • Protein or peptide: The heavy chain of 4A5
      • Protein or peptide: The light chain of 4A5
      • Protein or peptide: The heavy chain of 4H1
      • Protein or peptide: The light chain of 4H1
KeywordsSARS-CoV-2 / Neutralizing antibody / Cryo-EM / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / 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 / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsSun H / Jiang Y / Wang S / Zheng Z / Li S / Zheng Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1
Authors: Sun H / Jiang Y / Wang S / Zheng Z / Li S / Zheng Q
History
DepositionDec 5, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62591.png

Downloads & links

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Map

FileDownload / File: emd_62591.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 260. Å		0.65 Å/pix.
x 400 pix.
= 260. Å		0.65 Å/pix.
x 400 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.07528189 - 1.8760766
Average (Standard dev.)0.0008212838 (±0.01773963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62591_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_62591_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 protoype spike protein in complex with triple-nAb 4H1,...

EntireName: SARS-CoV-2 protoype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1
Components
  • Complex: SARS-CoV-2 protoype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1
    • Complex: SARS-CoV-2 prototype spike protein
      • Protein or peptide: Spike protein S1
    • Complex: The fragments of triple-nAb 4H1, 4A5 and 4C1
      • Protein or peptide: The heavy chain of 4C1
      • Protein or peptide: The light chain of 4C1
      • Protein or peptide: The heavy chain of 4A5
      • Protein or peptide: The light chain of 4A5
      • Protein or peptide: The heavy chain of 4H1
      • Protein or peptide: The light chain of 4H1

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Supramolecule #1: SARS-CoV-2 protoype spike protein in complex with triple-nAb 4H1,...

SupramoleculeName: SARS-CoV-2 protoype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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

SupramoleculeName: SARS-CoV-2 prototype spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: The fragments of triple-nAb 4H1, 4A5 and 4C1

SupramoleculeName: The fragments of triple-nAb 4H1, 4A5 and 4C1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4, #6-#7
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: The heavy chain of 4C1

MacromoleculeName: The heavy chain of 4C1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 14.201554 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLVESGGG LAKPGGSLRL SCAASGFTFS SYWMNWVRQA PGKGLEWVSV INSGGDNAYY ADSVKGRFTT SRDNSKSTLS LQMNSLREE DTAVYYCAKD RNLYYYDSGY YTEFSFDYWG QGVLVTVSS

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Macromolecule #2: The light chain of 4C1

MacromoleculeName: The light chain of 4C1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.531521 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSVLTQPPSV SGDPGQSVTI SCTGSSSNIG GYYVNWYQQF PGTAPKLLIY DDNNRPSGVS DRFSGSKSGT SASLTITGLQ PGDEADYHC SGWDSSLSAV LFGRGTRLTV L

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Macromolecule #3: The heavy chain of 4A5

MacromoleculeName: The heavy chain of 4A5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.542273 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLVESGGG LVKPGGSLRL SCVASGFTFS DYEMHWVRQA PGKGLEWVSV ISESGGTTYY ADSVKGRFTI SRDNAKNSLF LQMNSLRAE DTAVYYCTRV VIVVFTAMRH FDYWGQGVLV TVSS

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Macromolecule #4: The light chain of 4A5

MacromoleculeName: The light chain of 4A5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.665923 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DIQMTQSPSS LSAPVGDTVT ITCRASQGIN SYLNWFQQKP GKAPKLLIYD ASTLESGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCL QYNNYPFTFG PGTRLDIK

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Macromolecule #5: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.772391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN ...String:
NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGP

UniProtKB: Spike glycoprotein

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Macromolecule #6: The heavy chain of 4H1

MacromoleculeName: The heavy chain of 4H1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 12.862414 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLQESGPG LVKPSETLSL SCAVSGASIS SYWWNWFRQS PGKGLEWIGK INGNSGITYY NPSLKSRLTI SKDASKKQLS LTLTSVTAA DTAVYFCATR DGNIVGVADY WGQGVLVTVS S

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Macromolecule #7: The light chain of 4H1

MacromoleculeName: The light chain of 4H1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 12.320703 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DVVMTQTPLS LPVTPGEPAS ISCRSSQSLF DGGHPYTSLD WYLQKPGQSP QLLIYMVSNR ASGVPDRFSG SASGTDFTLK ISRVEAEDV GVYFCMQSVE YPYSFGQGTT VDFK

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63770
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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