[English] 日本語
Yorodumi
- PDB-7qct: PDZ2 of LNX2 with SARS-CoV-2_E PBM complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qct
TitlePDZ2 of LNX2 with SARS-CoV-2_E PBM complex
Components
  • Envelope small membrane protein
  • Ligand of Numb protein X 2
KeywordsPROTEIN BINDING / PDZ2 of LNX2 with SARS-CoV-2_E PBM complex
Function / homology
Function and homology information


disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / cytoplasmic capsid assembly / Regulation of gap junction activity / neural precursor cell proliferation / host cell Golgi membrane / endoplasmic reticulum-Golgi intermediate compartment / Maturation of protein E ...disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / cytoplasmic capsid assembly / Regulation of gap junction activity / neural precursor cell proliferation / host cell Golgi membrane / endoplasmic reticulum-Golgi intermediate compartment / Maturation of protein E / PDZ domain binding / neuron differentiation / ubiquitin-protein transferase activity / monoatomic ion channel activity / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / structural constituent of virion / Attachment and Entry / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Envelope small membrane protein, SARS-CoV-2-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / PDZ domain ...Envelope small membrane protein, SARS-CoV-2-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Envelope small membrane protein / Ligand of Numb protein X 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.197 Å
AuthorsZhu, Y. / Alvarez, F. / Haouz, A. / Mechaly, A. / Caillet-Saguy, C.
Funding support France, 3items
OrganizationGrant numberCountry
Pasteur InstituteURGENCE COVID-19 fundraising campaign France
Agence Nationale de la Recherche (ANR)ANR Recherche Action Covid19 FRM PDZCov2 France
Pasteur InstituteDON MICHELIN COVID PFR-5 Cov-2-Cvnet France
CitationJournal: Front Microbiol / Year: 2022
Title: Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins.
Authors: Zhu, Y. / Alvarez, F. / Wolff, N. / Mechaly, A. / Brule, S. / Neitthoffer, B. / Etienne-Manneville, S. / Haouz, A. / Boeda, B. / Caillet-Saguy, C.
History
DepositionNov 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ligand of Numb protein X 2
B: Ligand of Numb protein X 2
C: Envelope small membrane protein
D: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)23,0764
Polymers23,0764
Non-polymers00
Water41423
1
A: Ligand of Numb protein X 2
C: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)11,5382
Polymers11,5382
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-6 kcal/mol
Surface area5540 Å2
MethodPISA
2
B: Ligand of Numb protein X 2
D: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)11,5382
Polymers11,5382
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-6 kcal/mol
Surface area5650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.23, 183.23, 183.23
Angle α, β, γ (deg.)90, 90, 90
Int Tables number211
Space group name H-MI432

-
Components

#1: Protein Ligand of Numb protein X 2 / Numb-binding protein 2 / PDZ domain-containing RING finger protein 1


Mass: 10210.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNX2, PDZRN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N448
#2: Protein/peptide Envelope small membrane protein / E / sM protein


Mass: 1327.508 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.55 Å3/Da / Density % sol: 77.85 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 2.5 M NaCl, 0.1 M sodium acetate PH 4.5, 0.2 M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.197→48.97 Å / Num. obs: 9009 / % possible obs: 99.69 % / Redundancy: 78.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2679 / Net I/σ(I): 20.81
Reflection shellResolution: 3.197→3.312 Å / Rmerge(I) obs: 3.061 / Num. unique obs: 861 / CC1/2: 0.459 / % possible all: 97.95

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EIY

5eiy


Resolution: 3.197→48.97 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.508 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.527 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.311
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 451 -RANDOM
Rwork0.2281 ---
obs0.2286 8993 99.8 %-
Displacement parametersBiso mean: 130.45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 3.197→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 0 23 1483
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081474HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.971984HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d540SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes258HARMONIC5
X-RAY DIFFRACTIONt_it1474HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion190SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1236SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion21.19
LS refinement shellResolution: 3.2→3.25 Å
RfactorNum. reflection% reflection
Rfree0.4842 21 -
Rwork0.385 --
obs0.39 409 95.92 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.94661.1871-1.80279.77991.040410.67060.01690.26220.71890.2622-0.1148-0.31640.7189-0.31640.0979-0.344-0.04370.032-0.39210.0073-0.446735.081-14.82783.6521
221.8357-13.323-4.45328.5013.781712.68562.3235-3.9046-0.6353-3.9046-2.033-0.9356-0.6353-0.9356-0.2905-0.03280.3716-0.0659-0.31060.0621-0.813425.21338.228673.2596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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