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- EMDB-32395: local structure of hu33 and spike -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-32395
Titlelocal structure of hu33 and spike
Map data
Sample
  • Complex: local structure of R33 and RBD
    • Protein or peptide: hu33 heavy chain
    • Protein or peptide: hu33 light chain
    • Protein or peptide: Surface glycoprotein
Function / homologyBetacoronavirus 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Surface glycoprotein
Function and homology information
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPulan L
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Signal Transduct Target Ther / Year: 2022
Title: A non-ACE2-blocking neutralizing antibody against Omicron-included SARS-CoV-2 variants.
Authors: Xiaomin Duan / Rui Shi / Pulan Liu / Qingrui Huang / Fengze Wang / Xinyu Chen / Hui Feng / Weijin Huang / Junyu Xiao / Jinghua Yan /
History
DepositionDec 15, 2021-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32395.png

Downloads & links

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Map

FileDownload / File: emd_32395.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: 0.242
Minimum - Maximum-1.0994354 - 1.7635144
Average (Standard dev.)-0.000343571 (±0.021783592)
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 : local structure of R33 and RBD

EntireName: local structure of R33 and RBD
Components
  • Complex: local structure of R33 and RBD
    • Protein or peptide: hu33 heavy chain
    • Protein or peptide: hu33 light chain
    • Protein or peptide: Surface glycoprotein

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Supramolecule #1: local structure of R33 and RBD

SupramoleculeName: local structure of R33 and RBD / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: hu33 heavy chain

MacromoleculeName: hu33 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.162599 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGSE LKKPGASVKV SCKASGYTFT DYGMNWVRQA PGQGLEWMGW INTYSGEPTY ADDFRGRFVF SLDTSVSTAY LQICSLKAE DTAVYYCARG GNWDWYFDVW GQGTLVTVS

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Macromolecule #2: hu33 light chain

MacromoleculeName: hu33 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.717014 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS NFLHWYQQKP GKAPKLLIYY ASQSISGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSNTWPLTFG QGTKLEIK

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Macromolecule #3: Surface glycoprotein

MacromoleculeName: Surface glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 20.745172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VKGFNCYFPL Q SYGFQPTY GVGYQPYRVV VLSFE

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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 222776
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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