[English] 日本語
Yorodumi
- EMDB-33045: SARS-CoV-2 spike glycoprotein in complex with neutralizing antibo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33045
TitleSARS-CoV-2 spike glycoprotein in complex with neutralizing antibody UT28K
Map data
Sample
  • Complex: SARS-COV-2 spike glycoprotein in complex with UT28K
    • Complex: SARS-CoV-2 spike glycoprotein
      • Protein or peptide: SARS-CoV-2 spike glycoprotein
    • Complex: UT28K Fab
      • Protein or peptide: UT28K Fab heavy chain
      • Protein or peptide: UT28K Fab light chain
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsOzawa T / Tani H / Anraku Y / Kita S / Igarashi E / Saga Y / Inasaki N / Kawasuji H / Yamada H / Sasaki S ...Ozawa T / Tani H / Anraku Y / Kita S / Igarashi E / Saga Y / Inasaki N / Kawasuji H / Yamada H / Sasaki S / Someoka M / Sasaki J / Hayakawa Y / Yamamoto Y / Morinaga Y / Kurosawa N / Isobe M / Fukuhara H / Maenaka K / Hashiguchi T / Kishi H / Kitajima I / Saito S / Niimi H
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101077 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101093 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)20H05773 Japan
Japan Science and TechnologyJPMJCR20H8 Japan
CitationJournal: MAbs / Year: 2022
Title: Novel super-neutralizing antibody UT28K is capable of protecting against infection from a wide variety of SARS-CoV-2 variants.
Authors: Tatsuhiko Ozawa / Hideki Tani / Yuki Anraku / Shunsuke Kita / Emiko Igarashi / Yumiko Saga / Noriko Inasaki / Hitoshi Kawasuji / Hiroshi Yamada / So-Ichiro Sasaki / Mayu Somekawa / Jiei ...Authors: Tatsuhiko Ozawa / Hideki Tani / Yuki Anraku / Shunsuke Kita / Emiko Igarashi / Yumiko Saga / Noriko Inasaki / Hitoshi Kawasuji / Hiroshi Yamada / So-Ichiro Sasaki / Mayu Somekawa / Jiei Sasaki / Yoshihiro Hayakawa / Yoshihiro Yamamoto / Yoshitomo Morinaga / Nobuyuki Kurosawa / Masaharu Isobe / Hideo Fukuhara / Katsumi Maenaka / Takao Hashiguchi / Hiroyuki Kishi / Isao Kitajima / Shigeru Saito / Hideki Niimi /
Abstract: Many potent neutralizing SARS-CoV-2 antibodies have been developed and used for therapies. However, the effectiveness of many antibodies has been reduced against recently emerging SARS-CoV-2 ...Many potent neutralizing SARS-CoV-2 antibodies have been developed and used for therapies. However, the effectiveness of many antibodies has been reduced against recently emerging SARS-CoV-2 variants, especially the Omicron variant. We identified a highly potent SARS-CoV-2 neutralizing antibody, UT28K, in COVID-19 convalescent individuals who recovered from a severe condition. UT28K showed efficacy in neutralizing SARS-CoV-2 in an assay and prophylactic treatment, and the reactivity to the Omicron strain was reduced. The structural analyses revealed that antibody UT28K Fab and SARS-CoV-2 RBD protein interactions were mainly chain-dominated antigen-antibody interactions. In addition, a mutation analysis suggested that the emergence of a UT28K neutralization-resistant SARS-CoV-2 variant was unlikely, as this variant would likely lose its competitive advantage over circulating SARS-CoV-2. Our data suggest that UT28K offers potent protection against SARS-CoV-2, including newly emerging variants.
History
DepositionMar 10, 2022-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateMay 25, 2022-
Current statusMay 25, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33045.png

Downloads & links

-
Map

FileDownload / File: emd_33045.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.00677
Minimum - Maximum-0.014139489 - 0.046714377
Average (Standard dev.)1.1384879e-05 (±0.0015658148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_33045_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33045_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_33045_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SARS-COV-2 spike glycoprotein in complex with UT28K

EntireName: SARS-COV-2 spike glycoprotein in complex with UT28K
Components
  • Complex: SARS-COV-2 spike glycoprotein in complex with UT28K
    • Complex: SARS-CoV-2 spike glycoprotein
      • Protein or peptide: SARS-CoV-2 spike glycoprotein
    • Complex: UT28K Fab
      • Protein or peptide: UT28K Fab heavy chain
      • Protein or peptide: UT28K Fab light chain

-
Supramolecule #1: SARS-COV-2 spike glycoprotein in complex with UT28K

SupramoleculeName: SARS-COV-2 spike glycoprotein in complex with UT28K / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 50 KDa

-
Supramolecule #2: SARS-CoV-2 spike glycoprotein

SupramoleculeName: SARS-CoV-2 spike glycoprotein / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Drosophila (fruit flies)

-
Supramolecule #3: UT28K Fab

SupramoleculeName: UT28K Fab / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #1: SARS-CoV-2 spike glycoprotein

MacromoleculeName: SARS-CoV-2 spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Drosophila (fruit flies)
SequenceString: SSQCVNLTTR TQLPPAYTNS FTRGVYYPDK VFRSSVLHST QDLFLPFFSN VTWFHAIHVS GTNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG ...String:
SSQCVNLTTR TQLPPAYTNS FTRGVYYPDK VFRSSVLHST QDLFLPFFSN VTWFHAIHVS GTNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LVRDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSYLTP GDSSSGWTAG AAAYYVGYLQ PRTFLLKYNE NGTITDAVDC ALDPLSETKC TLKSFTVEKG IYQTSNFRVQ PTESIVRFPN ITNLCPFGEV FNATRFASVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP LQSYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGPKKST NLVKNKCVNF NFNGLTGTGV LTESNKKFLP FQQFGRDIAD TTDAVRDPQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQDVNCTEVP VAIHADQLTP TWRVYSTGSN VFQTRAGCLI GAEHVNNSYE CDIPIGAGIC ASYQTQTQTN SPGSAGSVAS QSIIAYTMSL GAENSVAYSN NSIAIPTNFT ISVTTEILPV SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKDFGG FNFSQILPDP SKPSKRSPIE DLLFNKVTLA DAGFIKQYGD CLGDIAARDL ICAQKFNGLT VLPPLLTDEM IAQYTSALLA GTITSGWTFG AGPALQIPFP MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STPSALGKLQ DVVNQNAQAL NTLVKQLSSN FGAISSVLND ILSRLDPPEA EVQIDRLITG RLQSLQTYVT QQLIRAAEIR ASANLAATKM SECVLGQSKR VDFCGKGYHL MSFPQSAPHG VVFLHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFVSGNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQELGKYEQY I

-
Macromolecule #2: UT28K Fab heavy chain

MacromoleculeName: UT28K Fab heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDWIWRILFL VGAATGAHSQ MQLVQSGPEV KKPGTSVKVS CKASGFTFSI SAVQWVRQAR GQRLEWIGWI VVGSGNTNYA QKFQERVTIT RDMSTSTAYM ELSSLRFEDT AVYYCAAPYC GGDCSDGFDI WGQGTMVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV ...String:
MDWIWRILFL VGAATGAHSQ MQLVQSGPEV KKPGTSVKVS CKASGFTFSI SAVQWVRQAR GQRLEWIGWI VVGSGNTNYA QKFQERVTIT RDMSTSTAYM ELSSLRFEDT AVYYCAAPYC GGDCSDGFDI WGQGTMVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSGSSGHHH HHHHHHH

-
Macromolecule #3: UT28K Fab light chain

MacromoleculeName: UT28K Fab light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METPAQLLFL LLLWLPDTTG EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGNSPWTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK ...String:
METPAQLLFL LLLWLPDTTG EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYCQ QYGNSPWTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

-
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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 2217 / Average exposure time: 1.5 sec. / Average electron dose: 53.14 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 711242
CTF correctionSoftware - Name: RELION (ver. 3.1.3)
Startup modelType of model: OTHER
Details: the map of SARS-CoV-2 Spike glycoprotein close state reconstructed using EMPIAR-10514 dataset
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 56247
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more