[English] 日本語
Yorodumi
- PDB-7tpr: Camel nanobodies 7A3 and 8A2 broadly neutralize SARS-CoV-2 variants -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tpr
TitleCamel nanobodies 7A3 and 8A2 broadly neutralize SARS-CoV-2 variants
Components
  • Nanobody 7A3
  • Nanobody 8A2
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neutralization / nanobody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / 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 / identical protein binding / membrane / 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
Camelus dromedarius (Arabian camel)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsButay, K.J. / Zhu, J. / Dandey, V.P. / Hong, J. / Kwon, H.J. / Chen, C.Z. / Duan, Z. / Li, D. / Ren, H. / Liang, T. ...Butay, K.J. / Zhu, J. / Dandey, V.P. / Hong, J. / Kwon, H.J. / Chen, C.Z. / Duan, Z. / Li, D. / Ren, H. / Liang, T. / Martin, N. / Esposito, D. / Ortega-Rodriguez, U. / Xu, M. / Xie, H. / Ho, M. / Cachau, R. / Borgnia, M.J.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES 103341 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ZIA BC 011943 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC ES 10326 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ZIC BC 011891 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)Z01 BC010891 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ZIA BC010891 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)75N91019D00024 United States
CitationJournal: bioRxiv / Year: 2021
Title: Camel nanobodies broadly neutralize SARS-CoV-2 variants.
Authors: Jessica Hong / Hyung Joon Kwon / Raul Cachau / Catherine Z Chen / Kevin John Butay / Zhijian Duan / Dan Li / Hua Ren / Tianyuzhou Liang / Jianghai Zhu / Venkata P Dandey / Negin Martin / ...Authors: Jessica Hong / Hyung Joon Kwon / Raul Cachau / Catherine Z Chen / Kevin John Butay / Zhijian Duan / Dan Li / Hua Ren / Tianyuzhou Liang / Jianghai Zhu / Venkata P Dandey / Negin Martin / Dominic Esposito / Uriel Ortega-Rodriguez / Miao Xu / Mario J Borgnia / Hang Xie / Mitchell Ho /
Abstract: With the emergence of SARS-CoV-2 variants, there is urgent need to develop broadly neutralizing antibodies. Here, we isolate two V H nanobodies (7A3 and 8A2) from dromedary camels by phage display, ...With the emergence of SARS-CoV-2 variants, there is urgent need to develop broadly neutralizing antibodies. Here, we isolate two V H nanobodies (7A3 and 8A2) from dromedary camels by phage display, which have high affinity for the receptor-binding domain (RBD) and broad neutralization activities against SARS-CoV-2 and its emerging variants. Cryo-EM complex structures reveal that 8A2 binds the RBD in its up mode and 7A3 inhibits receptor binding by uniquely targeting a highly conserved and deeply buried site in the spike regardless of the RBD conformational state. 7A3 at a dose of ≥5 mg/kg efficiently protects K18-hACE2 transgenic mice from the lethal challenge of B.1.351 or B.1.617.2, suggesting that the nanobody has promising therapeutic potentials to curb the COVID-19 surge with emerging SARS-CoV-2 variants.
ONE-SENTENCE SUMMARY: Dromedary camel ( ) V H phage libraries were built for isolation of the nanobodies that broadly neutralize SARS-CoV-2 variants.
History
DepositionJan 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
D: Nanobody 8A2
E: Nanobody 8A2
F: Nanobody 7A3
G: Nanobody 7A3
H: Nanobody 7A3


Theoretical massNumber of molelcules
Total (without water)449,7178
Polymers449,7178
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 126821.453 Da / Num. of mol.: 3
Mutation: F817P, A892P, A899P, A942P, K986P, V987P, and residues 682-685 from RRAR to GSAS
Source method: isolated from a genetically manipulated source
Details: Hexa-Pro construct mutations
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody Nanobody 8A2


Mass: 13993.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#3: Antibody Nanobody 7A3


Mass: 13755.188 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Ternary complex of SARS-Cov-2 Spike protein ectodomain (Wuhan strain) and camel nanobodies 7A3 and 8A2.COMPLEXall0MULTIPLE SOURCES
2SARS-CoV-2 Spike glycoproteinCOMPLEX#11RECOMBINANT
3Camel nanobody 8A2COMPLEX#21RECOMBINANT
4Camel nanobody 7A3COMPLEX#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.45 MDaNO
210.44 MDaNO
310.017 MDaNO
410.017 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Severe acute respiratory syndrome coronavirus 22697049
43Camelus dromedarius (Arabian camel)9838
54Camelus dromedarius (Arabian camel)9838
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCell
32Homo sapiens (human)9606Expi293F
43Escherichia coli (E. coli)562HB2151
54Escherichia coli (E. coli)562HB2151
Buffer solutionpH: 7.5 / Details: PBS
SpecimenConc.: 1.93 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Complexes of spike with 7A3 and/or 8A2 VHHs were prepared by mixing the components at a spike trimer to nanobody molar ratio of 1:6. The final concentration of spike trimer was 3 uM in PBS ...Details: Complexes of spike with 7A3 and/or 8A2 VHHs were prepared by mixing the components at a spike trimer to nanobody molar ratio of 1:6. The final concentration of spike trimer was 3 uM in PBS at pH 7 with the addition of 5 mM imidazole. Because the 8A2 stock was too diluted, complexes involving this nanobody were prepared at 0.5 uM spike trimer followed by a 6-fold concentration using a 10 kDa cutoff centrifugal filter (Amicon Ultra). All complexes were incubated on ice for at least 5 min prior to grid preparation.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Homemade
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company /
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Alignment procedure: ZEMLIN TABLEAU / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1

IDAccelerating voltage (kV)C2 aperture diameter (µm)Calibrated magnification (X)CryogenModelNominal magnification (X)
12006053648NITROGENFEI TALOS ARCTICA45000
23005047348FEI TITAN KRIOS81000
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Detector modeFilm or detector model
11160COUNTINGGATAN K2 SUMMIT (4k x 4k)
2260GATAN K3 BIOQUANTUM (6k x 4k)
Image scansSampling size: 5.000001 µm / Width: 5760 / Height: 4092

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryImaging-ID
2SerialEM3image acquisition1
4cryoSPARC3.3CTF correction
10cryoSPARC3.3initial Euler assignment
11cryoSPARC3.3final Euler assignment
13cryoSPARC3.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1539054
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 580888 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00433397
ELECTRON MICROSCOPYf_angle_d0.57845472
ELECTRON MICROSCOPYf_dihedral_angle_d10.8044832
ELECTRON MICROSCOPYf_chiral_restr0.0455232
ELECTRON MICROSCOPYf_plane_restr0.0045822

+
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