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- PDB-7qcr: MLLT4/Afadin PDZ domain in complex with the C-terminal peptide fr... -

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Basic information

Entry
Database: PDB / ID: 7qcr
TitleMLLT4/Afadin PDZ domain in complex with the C-terminal peptide from protein E of SARS-CoV-2
Components
  • Afadin
  • Envelope small membrane protein
KeywordsCELL ADHESION / MLLT4-Afadin PDZ domain in complex with the C-terminal peptide from protein E of SARS-CoV-2
Function / homology
Function and homology information


disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / establishment of protein localization to plasma membrane / positive regulation of cell-cell adhesion mediated by cadherin / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / pore complex assembly / establishment of endothelial intestinal barrier / positive regulation of cell-cell adhesion / Regulation of gap junction activity ...disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / establishment of protein localization to plasma membrane / positive regulation of cell-cell adhesion mediated by cadherin / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / pore complex assembly / establishment of endothelial intestinal barrier / positive regulation of cell-cell adhesion / Regulation of gap junction activity / bicellular tight junction assembly / cell-cell contact zone / cell-cell adhesion mediated by cadherin / Adherens junctions interactions / tight junction / pore complex / host cell Golgi membrane / cell adhesion molecule binding / Maturation of protein E / negative regulation of cell migration / adherens junction / small GTPase binding / actin filament binding / cell junction / cell-cell junction / cell-cell signaling / regulation of protein localization / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / Attachment and Entry / cell adhesion / nuclear speck / cadherin binding / positive regulation of gene expression / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / signal transduction / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / Afadin, cargo binding 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. / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain ...: / Afadin, cargo binding 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. / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Envelope small membrane protein / Afadin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsZhu, Y. / Alvarez, F. / Haouz, A. / Mechaly, A. / Caillet-Saguy, C.
Funding support France, 2items
OrganizationGrant numberCountry
Pasteur InstituteURGENCE COVID-19 France
Agence Nationale de la Recherche (ANR)Recherche Action Covid19 FRM PDZCov2 program 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Afadin
B: Afadin
C: Envelope small membrane protein
D: Envelope small membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8785
Polymers22,7824
Non-polymers961
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-33 kcal/mol
Surface area9480 Å2
Unit cell
Length a, b, c (Å)76.16, 43.49, 56.07
Angle α, β, γ (deg.)90, 96.88, 90
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS oper: (Code: givenMatrix: (0.99015638853, -0.118219000272, 0.0749305960776), (-0.119214906114, -0.992828180042, 0.00894489094523), (0.0733357512682, -0.0177896848906, -0.9971486322)Vector: -1. ...NCS oper: (Code: given
Matrix: (0.99015638853, -0.118219000272, 0.0749305960776), (-0.119214906114, -0.992828180042, 0.00894489094523), (0.0733357512682, -0.0177896848906, -0.9971486322)
Vector: -1.70488894179, -25.4245093636, 28.6620310547)

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Components

#1: Protein Afadin / ALL1-fused gene from chromosome 6 protein / Protein AF-6 / Afadin adherens junction formation factor


Mass: 10063.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFDN, AF6, MLLT4 / Production host: Escherichia coli (E. coli) / References: UniProt: P55196
#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 1 M Na3 Citrate, 0.1 M TRIS at pH 7, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.28→37.81 Å / Num. obs: 8373 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 44.58 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.2185 / Net I/σ(I): 6.59
Reflection shellResolution: 2.281→2.362 Å / Rmerge(I) obs: 1.454 / Num. unique obs: 746 / CC1/2: 0.506

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AXA

3axa


Resolution: 2.28→37.81 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.377 / SU Rfree Blow DPI: 0.236 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 419 -RANDOM
Rwork0.2208 ---
obs0.2223 8373 98.9 %-
Displacement parametersBiso mean: 51.33 Å2
Baniso -1Baniso -2Baniso -3
1--9.7889 Å20 Å2-1.6374 Å2
2--4.0927 Å20 Å2
3---5.6962 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.28→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 5 74 1404
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081335HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.081794HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d484SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes223HARMONIC5
X-RAY DIFFRACTIONt_it1335HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion184SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1089SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion18.25
LS refinement shellResolution: 2.28→2.33 Å
RfactorNum. reflection% reflection
Rfree0.3242 21 -
Rwork0.2256 --
obs0.2304 419 81.84 %
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)
10.77970.24140.41023.4927-1.20053.95070.0319-0.283-0.0519-0.283-0.0517-0.0332-0.0519-0.03320.01980.29190.01580.08720.26080.00750.2901-15.6208-21.164619.913
20.86470.6015-1.00431.1104-2.67414.47840.0803-0.0409-0.0292-0.0409-0.0787-0.0445-0.0292-0.0445-0.00160.6213-0.00840.05640.3739-0.05120.3413-13.1498-2.24797.6983
30.470.2622-0.984901.24430.5091-0.23630.09110.04520.0911-0.03230.09270.04520.09270.26860.94450.03830.19650.4126-0.03510.4158-8.4065-2.179814.5633
40.1121-0.26170.44410.6927-0.32071.0319-0.0955-0.36840.1474-0.36840.12960.11840.14740.1184-0.03410.4383-0.0504-0.03980.53590.00440.5289-11.79-23.181214.0719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|91 }
2X-RAY DIFFRACTION2{ B|2 - B|91 }
3X-RAY DIFFRACTION3{ C|100 - C|104 }
4X-RAY DIFFRACTION4{ D|* }

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