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- EMDB-31635: CryoEM map of del68-76/del679-688 prefusion-stabilized spike in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-31635
TitleCryoEM map of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9
Map data
Sample
  • Complex: del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9
    • Complex: spike protein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: Fab of N12-9
      • Protein or peptide: the heavy chain of N12-9 Fab
      • Protein or peptide: the light chain of N12-9 Fab
  • 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
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 speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsDu S / Xiao J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9
Authors: Du S / Xiao J
History
DepositionAug 7, 2021-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31635.png

Downloads & links

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Map

FileDownload / File: emd_31635.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.424
Minimum - Maximum-1.7876692 - 3.4438775
Average (Standard dev.)0.00042055585 (±0.07037071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : del68-76/del679-688 prefusion-stabilized spike in complex with th...

EntireName: del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9
Components
  • Complex: del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9
    • Complex: spike protein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: Fab of N12-9
      • Protein or peptide: the heavy chain of N12-9 Fab
      • Protein or peptide: the light chain of N12-9 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: del68-76/del679-688 prefusion-stabilized spike in complex with th...

SupramoleculeName: del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

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Supramolecule #2: spike protein

SupramoleculeName: spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

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Supramolecule #3: Fab of N12-9

SupramoleculeName: Fab of N12-9 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 140.701641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAKRF DNPVLPFNDG VYFASTEKS NIIRGWIFGT TLDSKTQSLL IVNNATNVVI KVCEFQFCND PFLGVYYHKN NKSWMESEFR VYSSANNCTF E YVSQPFLM ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAKRF DNPVLPFNDG VYFASTEKS NIIRGWIFGT TLDSKTQSLL IVNNATNVVI KVCEFQFCND PFLGVYYHKN NKSWMESEFR VYSSANNCTF E YVSQPFLM DLEGKQGNFK NLREFVFKNI DGYFKIYSKH TPINLVRDLP QGFSALEPLV DLPIGINITR FQTLLALHRS YL TPGDSSS GWTAGAAAYY VGYLQPRTFL LKYNENGTIT DAVDCALDPL SETKCTLKSF TVEKGIYQTS NFRVQPTESI VRF PNITNL CPFGEVFNAT RFASVYAWNR KRISNCVADY SVLYNSASFS TFKCYGVSPT KLNDLCFTNV YADSFVIRGD EVRQ IAPGQ TGKIADYNYK LPDDFTGCVI AWNSNNLDSK VGGNYNYLYR LFRKSNLKPF ERDISTEIYQ AGSTPCNGVE GFNCY FPLQ SYGFQPTNGV GYQPYRVVVL SFELLHAPAT VCGPKKSTNL VKNKCVNFNF NGLTGTGVLT ESNKKFLPFQ QFGRDI ADT TDAVRDPQTL EILDITPCSF GGVSVITPGT NTSNQVAVLY QDVNCTEVPV AIHADQLTPT WRVYSTGSNV FQTRAGC LI GAEHVNNSYE CDIPIGAGIC ASYQTQTSQS IIAYTMSLGA ENSVAYSNNS IAIPTNFTIS VTTEILPVSM TKTSVDCT M YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSPIE DLLFNKVTLA DAGFIKQYGD CLGDIAARDL ICAQKFNGLT VLPPLLTDEM IAQYTSALLA GTITSGWTFG AGPALQIPFP MQMAYRFNG IGVTQNVLYE NQKLIANQFN SAIGKIQDSL SSTPSALGKL QDVVNQNAQA LNTLVKQLSS NFGAISSVLN D ILSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KRVDFCGKGY HLMSFPQSAP HG VVFLHVT YVPAQEKNFT TAPAICHDGK AHFPREGVFV SNGTHWFVTQ RNFYEPQIIT TDNTFVSGNC DVVIGIVNNT VYD PLQPEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLIDLQELGK YEQGSGYIPE APRD GQAYV RKDGEWVLLS TFLGRSLEVL FQGPGHHHHH HHHSAWSHPQ FEKGGGSGGG GSGGSAWSHP QFEK

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Macromolecule #2: the heavy chain of N12-9 Fab

MacromoleculeName: the heavy chain of N12-9 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.487923 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVKPGGSLRL SCAASEFTFS SYSMNWVRQA PGKGLEWVSS ISSSGSQIYY ADSVKGRFTI SRDNAKKSLY LQMNSLRVE DTAVYYCATN GGAHSSTWSF YGMDVWGQGT TVTVSS

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Macromolecule #3: the light chain of N12-9 Fab

MacromoleculeName: the light chain of N12-9 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.209329 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELTQPPSV SVSPGQTATI TCSGDKLGDK YACWYQQRPG QSPVLVIYQD SKRPSGIPER FSGSNSGNTA TLTIGGTQAM DEAAYFCQA WDSNTGVFGG GTKLTVL

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 28 / 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

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: DARK FIELD
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

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280380

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