[English] 日本語
Yorodumi
- EMDB-22738: CryoEM reconstruction of SARS-CoV-2 receptor binding domain in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22738
TitleCryoEM reconstruction of SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
Map dataFab 46 in complex with RBD domain of SARS-CoV-2 Spike protein.
Sample
  • Complex: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
    • Complex: Fab fragment of neutralizing antibody 46
      • Protein or peptide: Fab 46 heavy chain
      • Protein or peptide: Fab 46 light chain
    • Complex: SARS-CoV-2 receptor binding domain
      • Protein or peptide: Receptor Binding Domain of SARS-CoV-2 Spike
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsKucharska I / Tan YZ / Benlekbir S / Rubinstein JL / Julien JP
Funding support Canada, 5 items
OrganizationGrant numberCountry
Ontario Ministry of Colleges and UniversitiesCOVID-19 Research Fund C-094-2424972-JULIEN Canada
Canada Foundation for Innovation Canada
Ontario Research Fund Canada
The Hospital For Sick Children Foundation Canada
Canada Research Chairs program Canada
Citation
Journal: Nat Commun / Year: 2021
Title: Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers.
Authors: Edurne Rujas / Iga Kucharska / Yong Zi Tan / Samir Benlekbir / Hong Cui / Tiantian Zhao / Gregory A Wasney / Patrick Budylowski / Furkan Guvenc / Jocelyn C Newton / Taylor Sicard / Anthony ...Authors: Edurne Rujas / Iga Kucharska / Yong Zi Tan / Samir Benlekbir / Hong Cui / Tiantian Zhao / Gregory A Wasney / Patrick Budylowski / Furkan Guvenc / Jocelyn C Newton / Taylor Sicard / Anthony Semesi / Krithika Muthuraman / Amy Nouanesengsy / Clare Burn Aschner / Katherine Prieto / Stephanie A Bueler / Sawsan Youssef / Sindy Liao-Chan / Jacob Glanville / Natasha Christie-Holmes / Samira Mubareka / Scott D Gray-Owen / John L Rubinstein / Bebhinn Treanor / Jean-Philippe Julien /
Abstract: SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a ...SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers. Using this platform, half-maximal inhibitory concentration (IC) values as low as 9 × 10 M are achieved as a result of up to 10,000-fold potency enhancements compared to corresponding IgGs. Combination of three different antibody specificities and the fragment crystallizable (Fc) domain on a single multivalent molecule conferred the ability to overcome viral sequence variability together with outstanding potency and IgG-like bioavailability. The MULTi-specific, multi-Affinity antiBODY (Multabody or MB) platform thus uniquely leverages binding avidity together with multi-specificity to deliver ultrapotent and broad neutralizers against SARS-CoV-2. The modularity of the platform also makes it relevant for rapid evaluation against other infectious diseases of global health importance. Neutralizing antibodies are a promising therapeutic for SARS-CoV-2.
#1: Journal: Biorxiv / Year: 2020
Title: Multivalency transforms SARS-CoV-2 antibodies into broad and ultrapotent neutralizers
Authors: Rujas E / Kucharska I / Tan YZ / Benlekbir S / Cui H / Zhao T / Wasney G / Budylowski P / Guvenc F / Newton J / Semesi A / Muthuraman K / Nouanesengsy A / Prieto K / Bueler S / Youssef S / ...Authors: Rujas E / Kucharska I / Tan YZ / Benlekbir S / Cui H / Zhao T / Wasney G / Budylowski P / Guvenc F / Newton J / Semesi A / Muthuraman K / Nouanesengsy A / Prieto K / Bueler S / Youssef S / Liao-Chan S / Glanville J / Christie-Holmes N / Mubareka S / Gray-Owen SD / Rubinstein JL / Treanor B / Julien JP
History
DepositionSep 28, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 3.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22738.png

Downloads & links

-
Map

FileDownload / File: emd_22738.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFab 46 in complex with RBD domain of SARS-CoV-2 Spike protein.
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 3.4 / Movie #1: 3.4
Minimum - Maximum-9.889899 - 19.365408
Average (Standard dev.)0.0036772892 (±0.6295338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 206.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z206.000206.000206.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-9.89019.3650.004

-
Supplemental data

-
Sample components

-
Entire : SARS-CoV-2 receptor binding domain in complex with the Fab fragme...

EntireName: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
Components
  • Complex: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
    • Complex: Fab fragment of neutralizing antibody 46
      • Protein or peptide: Fab 46 heavy chain
      • Protein or peptide: Fab 46 light chain
    • Complex: SARS-CoV-2 receptor binding domain
      • Protein or peptide: Receptor Binding Domain of SARS-CoV-2 Spike

-
Supramolecule #1: SARS-CoV-2 receptor binding domain in complex with the Fab fragme...

SupramoleculeName: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Fab fragment of neutralizing antibody 46

SupramoleculeName: Fab fragment of neutralizing antibody 46 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

-
Supramolecule #3: SARS-CoV-2 receptor binding domain

SupramoleculeName: SARS-CoV-2 receptor binding domain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #1: Fab 46 heavy chain

MacromoleculeName: Fab 46 heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGG LVQPGRSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVST IYSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARGD S RDAFDIWG QGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YF PEPVTVS WNSGALTSGV ...String:
EVQLLESGGG LVQPGRSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVST IYSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARGD S RDAFDIWG QGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YF PEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YIC NVNHKP SNTKVDKKVE PKSC

-
Macromolecule #2: Fab 46 light chain

MacromoleculeName: Fab 46 light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYD ASNLETGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYCQ QSYSTPFTFG P GTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYD ASNLETGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYCQ QSYSTPFTFG P GTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQG LSSPVT KSFNRGEC

-
Macromolecule #3: Receptor Binding Domain of SARS-CoV-2 Spike

MacromoleculeName: Receptor Binding Domain of SARS-CoV-2 Spike / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC ...String:
RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC YFPLQSYGFQ PTNGVGYQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFHHHHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3TRIS
150.0 mMNaClsodium chloride
0.02 %NaN3sodium azide
GridModel: Homemade / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: glow discharged with PELCO easiGlow (Ted Pella)
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 4722 / Average exposure time: 9.6 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3402345
CTF correctionSoftware - Name: cryoSPARC (ver. 2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 32283
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2)

+
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://pdbjlvh1.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