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- EMDB-16026: SARS-CoV-2 S protein in complex with pT1696 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-16026
TitleSARS-CoV-2 S protein in complex with pT1696 Fab
Map datafocus map
Sample
  • Complex: 3:3 pT1696 Fab-Spike complex
    • Complex: pT1696 Fab
      • Protein or peptide: pT1696 Fab heavy chain
      • Protein or peptide: pT1696 Fab light chain
    • Complex: Spike protein S1
      • Protein or peptide: Spike glycoproteinSpike protein
KeywordsPROTEIN BINDING/IMMUNE SYSTEM / PROTEIN BINDING
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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsHansen G / Benecke T / Vollmer B / Gruenewald K / Krey T
Funding support Germany, 6 items
OrganizationGrant numberCountry
Other government14-76103-184 CORONA-12/20 Germany
Other government14-76103-184 CORONA-15/20 Germany
German Federal Ministry for Education and ResearchCOVIM (FKZ: 01KX2021) Germany
German Federal Ministry for Education and ResearchRAPID (FKZ: 01KI1723G) Germany
German Research Foundation (DFG)EXC 2155 Germany
German Research Foundation (DFG)2485 VIPER (398066876/GRK 2485/1) Germany
CitationJournal: To be published
Title: Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?
Authors: Stein CS / Hansen G / Ssebyatika GL / Stroeh L / Benecke T / Menz S / Waldmann J-Y / Vollmer B / Tipp S / Ochulor O / Herold E / Schwarzloh B / Mutschall D / Zischke J-Y / Cordes A / Puppe W ...Authors: Stein CS / Hansen G / Ssebyatika GL / Stroeh L / Benecke T / Menz S / Waldmann J-Y / Vollmer B / Tipp S / Ochulor O / Herold E / Schwarzloh B / Mutschall D / Zischke J-Y / Cordes A / Puppe W / Schneider T / Hinrichs I / Blasczyk R / Kleine-Weber H / Hoffmann M / Hoeper M / Kaiser FK / Gonzalez-Hernandez M / Armando FK / Ciurkiewicz M / Beythien G / Poehlmann S / Baumgaertner W / Gruenewald K / Osterhaus A / Schulz T / Krey T
History
DepositionOct 27, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16026.png

Downloads & links

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Map

FileDownload / File: emd_16026.map.gz / Format: CCP4 / Size: 104.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 355 pix.
= 241.4 Å		0.68 Å/pix.
x 290 pix.
= 197.2 Å		0.68 Å/pix.
x 267 pix.
= 181.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0017970094 - 1.8855299
Average (Standard dev.)0.001158711 (±0.024383558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin213143242
Dimensions290267355
Spacing267290355
CellA: 181.56 Å / B: 197.2 Å / C: 241.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: focus map, local filter

Fileemd_16026_additional_1.map
Annotationfocus map, local filter
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16026_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_16026_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 : 3:3 pT1696 Fab-Spike complex

EntireName: 3:3 pT1696 Fab-Spike complex
Components
  • Complex: 3:3 pT1696 Fab-Spike complex
    • Complex: pT1696 Fab
      • Protein or peptide: pT1696 Fab heavy chain
      • Protein or peptide: pT1696 Fab light chain
    • Complex: Spike protein S1
      • Protein or peptide: Spike glycoproteinSpike protein

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Supramolecule #1: 3:3 pT1696 Fab-Spike complex

SupramoleculeName: 3:3 pT1696 Fab-Spike complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: pT1696 Fab

SupramoleculeName: pT1696 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Spike protein S1

SupramoleculeName: Spike protein S1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 140.749328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP F LMDLEGKQ ...String:
VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP F LMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPINLV RDLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SS SGWTAGA AAYYVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TESIVRFPNI TNL CPFGEV FNATRFASVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQT GKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSY GFQP TNGVGYQPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLTGT GVLTESNKKF LPFQQFGRDI ADTTDA VRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQDVNCT EVPVAIHADQ LTPTWRVYST GSNVFQTRAG CLIGAEH VN NSYECDIPIG AGICASYQTQ TNSPGSASSV ASQSIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTEIL PVSMTKTS V DCTMYICGDS TECSNLLLQY GSFCTQLNRA LTGIAVEQDK NTQEVFAQVK QIYKTPPIKD FGGFNFSQIL PDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA LGKLQDVVNQ NAQALNTLVK QLSSNFGAIS S VLNDILSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QS APHGVVF LHVTYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGNCDVVIGI VNN TVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDLQ ELGKYEQGSG YIPE APRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQFEK

UniProtKB: Spike glycoprotein

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Macromolecule #2: pT1696 Fab heavy chain

MacromoleculeName: pT1696 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.103283 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: QMQLEQSGPE VKKPGTSVKV SCKASGFTFS SAAVQWVRQA RGQRLEWMGW IVVGSGNANY AQKFQERVTI TRDMSTSIAY MELSSLRSE DTAVYYCAAP HCNRTSCLDG FDIWGQGTMV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QMQLEQSGPE VKKPGTSVKV SCKASGFTFS SAAVQWVRQA RGQRLEWMGW IVVGSGNANY AQKFQERVTI TRDMSTSIAY MELSSLRSE DTAVYYCAAP HCNRTSCLDG FDIWGQGTMV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRVEPKSCDK TDDDDKAGWS HP QFEKGGG SGGGSGGGSW SHPQFEK

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Macromolecule #3: pT1696 Fab light chain

MacromoleculeName: pT1696 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.701223 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: ASEIVLTQSP GTLSLSPGER ATLSCRASQS VSRNYLAWYQ QKPGQAPRLL IYGASSRATG IPDRFSGSGS GTDFTLNISR LEPEDFAVY YCQQYGSSPW TFGQGTKVDI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
ASEIVLTQSP GTLSLSPGER ATLSCRASQS VSRNYLAWYQ QKPGQAPRLL IYGASSRATG IPDRFSGSGS GTDFTLNISR LEPEDFAVY YCQQYGSSPW TFGQGTKVDI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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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

Concentration0.34 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 241184
FSC plot (resolution estimation)

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