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- EMDB-31378: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD... -

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Basic information

Entry
Database: EMDB / ID: EMD-31378
TitleLocal CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab
Map data
Sample
  • Complex: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: BD-821H
    • Protein or peptide: BD-821L
    • Protein or peptide: BD-771H
    • Protein or peptide: BD-771L
KeywordsSARS-COV2 / 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 / host extracellular space / viral translation / 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 / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / 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, 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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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, 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. / 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 S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 speciesHuman coronavirus 229E / Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / Resolution: 3.4 Å
AuthorsZhang ZY
CitationJournal: Cell Res / Year: 2021
Title: Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants.
Authors: Shuo Du / Pulan Liu / Zhiying Zhang / Tianhe Xiao / Ayijiang Yasimayi / Weijin Huang / Youchun Wang / Yunlong Cao / Xiaoliang Sunney Xie / Junyu Xiao /
History
DepositionMay 29, 2021-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.518
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.518
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ey5
  • Surface level: 0.518
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ey5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31378.png

Downloads & links

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Map

FileDownload / File: emd_31378.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.)
1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.518 / Movie #1: 0.518
Minimum - Maximum-4.7657356 - 6.974218
Average (Standard dev.)-0.00050111074 (±0.03927255)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 436.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z436.000436.000436.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-113-15
NX/NY/NZ10616274
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-4.7666.974-0.001

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Supplemental data

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Sample components

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Entire : Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD...

EntireName: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab
Components
  • Complex: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: BD-821H
    • Protein or peptide: BD-821L
    • Protein or peptide: BD-771H
    • Protein or peptide: BD-771L

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Supramolecule #1: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD...

SupramoleculeName: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human coronavirus 229E

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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: 142.066094 KDa
Recombinant expressionOrganism: Phaseolus vulgaris (common bean)
SequenceString: MFVFLVLLPL VSSQCVNFTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFA NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNFTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFA NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRGLPQ GFSALEPLVD LPIGINITRF QT LHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIR GDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGV KGFN CYFPLQSYGF QPTYGVGYQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEH VNNSYECDIP IGAGICASYQ TQTNSPGSAS SVASQSIIAY TMSLGVENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLN RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KDFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV NQNAQALNTL V KQLSSNFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSH PQFE K

UniProtKB: Spike glycoprotein

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Macromolecule #2: BD-821H

MacromoleculeName: BD-821H / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.878969 KDa
Recombinant expressionOrganism: Phaseolus vulgaris (common bean)
SequenceString: ELQLVQSGAE VKKPGESLKI SCKYSGNISP NFWIGWVRQM AGKGLEWMGI IYPDDSDSRY SPSFQGQVII SADKSITTAL LHWSSLKVS DTAKYYCVYG SGSPSNWFHP WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
ELQLVQSGAE VKKPGESLKI SCKYSGNISP NFWIGWVRQM AGKGLEWMGI IYPDDSDSRY SPSFQGQVII SADKSITTAL LHWSSLKVS DTAKYYCVYG SGSPSNWFHP WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKHHH HHH

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Macromolecule #3: BD-821L

MacromoleculeName: BD-821L / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.689248 KDa
Recombinant expressionOrganism: Phaseolus vulgaris (common bean)
SequenceString: EVVMTQSPAT LSVSPGERAT LSCRASQSVR YNLAWYQQKP GQAPRLLIYD ASTRATGIPG RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QYDNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EVVMTQSPAT LSVSPGERAT LSCRASQSVR YNLAWYQQKP GQAPRLLIYD ASTRATGIPG RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QYDNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: BD-771H

MacromoleculeName: BD-771H / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.0751 KDa
Recombinant expressionOrganism: Phaseolus vulgaris (common bean)
SequenceString: EVQLVESGGG FVKPGGSLRL SCAASGFKFS DAWMNWVRQA PGKGLEWVGR IKSKADGQTT DYAAPVKGRF SISRDDSKNT LFLQIHNLE SDDTAVYYCT TGALVESRYF DWFTGYYFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
EVQLVESGGG FVKPGGSLRL SCAASGFKFS DAWMNWVRQA PGKGLEWVGR IKSKADGQTT DYAAPVKGRF SISRDDSKNT LFLQIHNLE SDDTAVYYCT TGALVESRYF DWFTGYYFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKHHH HH H

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Macromolecule #5: BD-771L

MacromoleculeName: BD-771L / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.281967 KDa
Recombinant expressionOrganism: Phaseolus vulgaris (common bean)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRTSQGIY NYLAWYQQKP GKVPKLLIYG ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYKSAPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRTSQGIY NYLAWYQQKP GKVPKLLIYG ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYKSAPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 425986
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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