[English] 日本語
Yorodumi
- PDB-8aaa: Crystal structure of SARS-CoV-2 S RBD in complex with a stapled p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8aaa
TitleCrystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
Components
  • Spike protein S1
  • Stapled peptide
KeywordsVIRAL PROTEIN / sRBD / Stapled peptide
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Chem-29N / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrear, P. / Chen, L. / Gaynor, K. / Harman, M. / Dods, R. / Hyvonen, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2023
Title: Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2.
Authors: Gaynor, K.U. / Vaysburd, M. / Harman, M.A.J. / Albecka, A. / Jeffrey, P. / Beswick, P. / Papa, G. / Chen, L. / Mallery, D. / McGuinness, B. / Van Rietschoten, K. / Stanway, S. / Brear, P. / ...Authors: Gaynor, K.U. / Vaysburd, M. / Harman, M.A.J. / Albecka, A. / Jeffrey, P. / Beswick, P. / Papa, G. / Chen, L. / Mallery, D. / McGuinness, B. / Van Rietschoten, K. / Stanway, S. / Brear, P. / Lulla, A. / Ciazynska, K. / Chang, V.T. / Sharp, J. / Neary, M. / Box, H. / Herriott, J. / Kijak, E. / Tatham, L. / Bentley, E.G. / Sharma, P. / Kirby, A. / Han, X. / Stewart, J.P. / Owen, A. / Briggs, J.A.G. / Hyvonen, M. / Skynner, M.J. / James, L.C.
History
DepositionJun 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
B: Stapled peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0923
Polymers23,8372
Non-polymers2551
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-6 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.2, 112.2, 35.534
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

-
Components

#1: Protein Spike protein S1


Mass: 22074.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC2
#2: Protein/peptide Stapled peptide


Mass: 1762.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-29N / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)triprop-2-en-1-one, bound form


Mass: 255.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 22% PEGSM, 2% Glycerol, 0.01M CoCl2, 0.2M MgCl2, 0.1M Bis TRIS
PH range: 8 / Temp details: l

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.848→97.168 Å / Num. obs: 13749 / % possible obs: 91.5 % / Redundancy: 19.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.058 / Rrim(I) all: 0.254 / Net I/σ(I): 9.3 / Num. measured all: 266723
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.848-2.06815.51.693106446860.8630.4421.7511.965.2
6.039-97.168180.093123516850.9980.0220.09623.7100
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CJF

7cjf


Resolution: 1.9→48.58 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 924 -RANDOM
Rwork0.2267 ---
obs0.2272 18189 88.9 %-
Displacement parametersBiso mean: 51.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.6688 Å20 Å20 Å2
2--0.6688 Å20 Å2
3----1.3377 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 104 1771
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081733HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.932358HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d568SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes297HARMONIC5
X-RAY DIFFRACTIONt_it1733HARMONIC10
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion213SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1576SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion16.76
LS refinement shellResolution: 1.9→1.94 Å
RfactorNum. reflection% reflection
Rfree0.9356 4 -
Rwork0.8111 --
obs0.8137 396 29.54 %

+
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