[English] 日本語
Yorodumi
- EMDB-28189: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28189
TitleSARS-CoV-2 Spike in complex with biparatopic nanobody BP10
Map dataSARS-CoV-2 Spike in complex with biparatopic nanobody BP10
Sample
  • Complex: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10
    • Complex: SARS-CoV-2 Spike
      • Protein or peptide: SARS-CoV-2 Spike
    • Complex: BP10 Biparatopic Nanobody
      • Protein or peptide: BP10 Biparatopic Nanobody
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsPymm PG / Glukhova A / Tham WH
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: iScience / Year: 2022
Title: Biparatopic nanobodies targeting the receptor binding domain efficiently neutralize SARS-CoV-2.
Authors: Phillip Pymm / Samuel J Redmond / Olan Dolezal / Francesca Mordant / Ester Lopez / James P Cooney / Kathryn C Davidson / Ebene R Haycroft / Chee Wah Tan / Rebecca Seneviratna / Samantha L ...Authors: Phillip Pymm / Samuel J Redmond / Olan Dolezal / Francesca Mordant / Ester Lopez / James P Cooney / Kathryn C Davidson / Ebene R Haycroft / Chee Wah Tan / Rebecca Seneviratna / Samantha L Grimley / Damian F J Purcell / Stephen J Kent / Adam K Wheatley / Lin-Fa Wang / Andrew Leis / Alisa Glukhova / Marc Pellegrini / Amy W Chung / Kanta Subbarao / Adam P Uldrich / Wai-Hong Tham / Dale I Godfrey / Nicholas A Gherardin /
Abstract: The development of therapeutics to prevent or treat COVID-19 remains an area of intense focus. Protein biologics, including monoclonal antibodies and nanobodies that neutralize virus, have potential ...The development of therapeutics to prevent or treat COVID-19 remains an area of intense focus. Protein biologics, including monoclonal antibodies and nanobodies that neutralize virus, have potential for the treatment of active disease. Here, we have used yeast display of a synthetic nanobody library to isolate nanobodies that bind the receptor-binding domain (RBD) of SARS-CoV-2 and neutralize the virus. We show that combining two clones with distinct binding epitopes within the RBD into a single protein construct to generate biparatopic reagents dramatically enhances their neutralizing capacity. Furthermore, the biparatopic nanobodies exhibit enhanced control over clinically relevant RBD variants that escaped recognition by the individual nanobodies. Structural analysis of biparatopic binding to spike (S) protein revealed a unique binding mode whereby the two nanobody paratopes bridge RBDs encoded by distinct S trimers. Accordingly, biparatopic nanobodies offer a way to rapidly generate powerful viral neutralizers with enhanced ability to control viral escape mutants.
History
DepositionSep 19, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28189.png

Downloads & links

-
Map

FileDownload / File: emd_28189.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 Spike in complex with biparatopic nanobody BP10
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.8165962 - 1.5224991
Average (Standard dev.)-0.0003756255 (±0.036487352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions504504504
Spacing504504504
CellA=B=C: 665.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10

Fileemd_28189_half_map_1.map
AnnotationSARS-CoV-2 Spike in complex with biparatopic nanobody BP10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10

Fileemd_28189_half_map_2.map
AnnotationSARS-CoV-2 Spike in complex with biparatopic nanobody BP10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SARS-CoV-2 Spike in complex with biparatopic nanobody BP10

EntireName: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10
Components
  • Complex: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10
    • Complex: SARS-CoV-2 Spike
      • Protein or peptide: SARS-CoV-2 Spike
    • Complex: BP10 Biparatopic Nanobody
      • Protein or peptide: BP10 Biparatopic Nanobody

-
Supramolecule #1: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10

SupramoleculeName: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 1 MDa

-
Supramolecule #2: SARS-CoV-2 Spike

SupramoleculeName: SARS-CoV-2 Spike / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Supramolecule #3: BP10 Biparatopic Nanobody

SupramoleculeName: BP10 Biparatopic Nanobody / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Vicugna pacos (alpaca)

-
Macromolecule #1: SARS-CoV-2 Spike

MacromoleculeName: SARS-CoV-2 Spike / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQDVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEHVNNSY ECDIPIGAGI CASYQTQTNS PASVGSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GAALQIPFAM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQ

-
Macromolecule #2: BP10 Biparatopic Nanobody

MacromoleculeName: BP10 Biparatopic Nanobody / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG LVQAGGSLRL SCAASGIIFG RNAMGWYRQA PGKERELVAA ITRNGGSTYY ADSVKGRFTI SRDNAKNTVY LQMNSLKPED TAVYYCNADP YIATYDYWGQ GTQVTVSSGG GGSGGGGSQV QLVESGGGLV QAGGSLRLSC AASGSTFWFY AMGWYRQAPG ...String:
QVQLVESGGG LVQAGGSLRL SCAASGIIFG RNAMGWYRQA PGKERELVAA ITRNGGSTYY ADSVKGRFTI SRDNAKNTVY LQMNSLKPED TAVYYCNADP YIATYDYWGQ GTQVTVSSGG GGSGGGGSQV QLVESGGGLV QAGGSLRLSC AASGSTFWFY AMGWYRQAPG KERELVAAIS YSGSSTYYAD SVKGRFTISR DNAKNTVYLQ MNSLKPEDTA VYYCAKRNGV SYNYLALTNE EYDYWGQGTQ VTVSS

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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: 0.4 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14126
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