[English] 日本語
Yorodumi
- PDB-7zr2: Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zr2
TitleCrystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
Components
  • Spike protein S2'
  • Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1
KeywordsANTIVIRAL PROTEIN / coiled-coil
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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / 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 / endocytosis involved in viral entry into host cell / receptor ligand activity / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsCamara-Artigas, A. / Gavira, J.A. / Cano-Munoz, M. / Polo-Megias, D. / Conejero-Lara, F.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other governmentCV-26565 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity.
Authors: Cano-Munoz, M. / Polo-Megias, D. / Camara-Artigas, A. / Gavira, J.A. / Lopez-Rodriguez, M.J. / Laumond, G. / Schmidt, S. / Demiselle, J. / Bahram, S. / Moog, C. / Conejero-Lara, F.
History
DepositionMay 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Jan 21, 2026Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_nonpoly_scheme / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1
B: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)31,2512
Polymers31,2512
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-27 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.777, 37.374, 43.911
Angle α, β, γ (deg.)90.000, 95.670, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

-
Components

#1: Protein Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1


Mass: 26577.713 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 / Plasmid: pET303 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC2
#2: Protein/peptide Spike protein S2'


Mass: 4673.132 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide V39E derived from the S2 HR2 sequence.The amino terminal is acetylated and the carboxyl-terminal is amidated. The peptide was C-terminally tagged with a SGGY sequence to ...Details: Synthetic peptide V39E derived from the S2 HR2 sequence.The amino terminal is acetylated and the carboxyl-terminal is amidated. The peptide was C-terminally tagged with a SGGY sequence to confer UV absorption at 280 nm.
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 % / Mosaicity: 0.13 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M sodium HEPES, 20% (w/v) PEG4000, 10% (v/v) isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.45→18.92 Å / Num. obs: 46236 / % possible obs: 96.3 % / Redundancy: 3 % / Biso Wilson estimate: 15.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.039 / Rrim(I) all: 0.071 / Net I/σ(I): 9.4 / Num. measured all: 138163 / Scaling rejects: 18
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
1.45-1.482.40.786460319300.6160.5750.981.275.4
7.67-18.923.10.0299503050.9990.0180.03526.386.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LXT

6lxt


Resolution: 1.45→18.8 Å / SU ML: 0.1672 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 21.6976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.209 2265 4.9 %
Rwork0.174 43922 -
obs0.1757 46187 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.63 Å2
Refinement stepCycle: LAST / Resolution: 1.45→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 0 304 2318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732036
X-RAY DIFFRACTIONf_angle_d0.71692745
X-RAY DIFFRACTIONf_chiral_restr0.048332
X-RAY DIFFRACTIONf_plane_restr0.0046364
X-RAY DIFFRACTIONf_dihedral_angle_d14.7438767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.31291060.27652149X-RAY DIFFRACTION75.67
1.48-1.520.27971250.23272567X-RAY DIFFRACTION89.38
1.52-1.550.26361510.21722701X-RAY DIFFRACTION96.25
1.55-1.60.26661400.20012819X-RAY DIFFRACTION99.53
1.6-1.640.23871620.17872843X-RAY DIFFRACTION99.5
1.64-1.70.22661620.17672788X-RAY DIFFRACTION98.93
1.7-1.760.22351570.16822794X-RAY DIFFRACTION98.86
1.76-1.830.21541240.16222831X-RAY DIFFRACTION98.7
1.83-1.910.21981370.15812822X-RAY DIFFRACTION99.06
1.91-2.010.22211270.16532814X-RAY DIFFRACTION98.59
2.01-2.140.20271620.14742779X-RAY DIFFRACTION97.55
2.14-2.30.17411440.14832822X-RAY DIFFRACTION98.31
2.3-2.530.18451530.15332781X-RAY DIFFRACTION97.7
2.53-2.90.20761360.16942809X-RAY DIFFRACTION96.68
2.9-3.650.20861430.17272793X-RAY DIFFRACTION96.45
3.65-18.80.19531360.19092810X-RAY DIFFRACTION94.09

+
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