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- PDB-9hm2: A swapped dimeric form of ZO1/TJP1 PDZ2 in complex with the C-ter... -

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Basic information

Entry
Database: PDB / ID: 9hm2
TitleA swapped dimeric form of ZO1/TJP1 PDZ2 in complex with the C-terminal peptide from protein E of SARS-CoV-2
Components
  • Envelope small membrane protein
  • Tight junction protein ZO-1
KeywordsCELL ADHESION / PDZ2 / SCAFFOLDING / TIGHT JUNCTION
Function / homology
Function and homology information


disruption of cellular anatomical structure in another organism / symbiont-mediated perturbation of host cell endomembrane system / viral budding from Golgi membrane / positive regulation of blood-brain barrier permeability / adherens junction maintenance / RUNX1 regulates expression of components of tight junctions / positive regulation of cell-cell adhesion mediated by cadherin / ameloblast differentiation / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction ...disruption of cellular anatomical structure in another organism / symbiont-mediated perturbation of host cell endomembrane system / viral budding from Golgi membrane / positive regulation of blood-brain barrier permeability / adherens junction maintenance / RUNX1 regulates expression of components of tight junctions / positive regulation of cell-cell adhesion mediated by cadherin / ameloblast differentiation / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / protein localization to cell-cell junction / regulation of cell junction assembly / establishment of endothelial intestinal barrier / Regulation of gap junction activity / protein localization to bicellular tight junction / gap junction / protein localization to adherens junction / Apoptotic cleavage of cell adhesion proteins / cell-cell junction organization / actomyosin structure organization / cell-cell junction assembly / Signaling by Hippo / negative regulation of stress fiber assembly / tight junction / podosome / regulation of bicellular tight junction assembly / apical junction complex / maintenance of blood-brain barrier / positive regulation of sprouting angiogenesis / regulation of cytoskeleton organization / host cell Golgi membrane / bicellular tight junction / cell adhesion molecule binding / Maturation of protein E / cell projection / adherens junction / cell-cell adhesion / apical part of cell / cell junction / actin cytoskeleton organization / basolateral plasma membrane / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / Attachment and Entry / calmodulin binding / positive regulation of cell migration / cadherin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / protein-containing complex / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
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. / Tight junction protein ZO-1 / ZO-1, SH3 domain / Tight junction protein ZO / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 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. / Tight junction protein ZO-1 / ZO-1, SH3 domain / Tight junction protein ZO / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IODIDE ION / Envelope small membrane protein / Tight junction protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsAlvarez, F. / Mechaly, A. / Haouz, A. / Caillet-Saguy, C.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur InstituteDON MICHELIN COVID PFR-5 Cov-2-Cvnet France
CitationJournal: Biorxiv / Year: 2025
Title: HTRF-based identification of small molecules targeting SARS-CoV-2 E protein interaction with ZO-1 PDZ2
Authors: Alvarez, F. / Larrous, F. / Mechaly, A. / Bardiaux, B. / Goor, Q. / Haouz, A. / Seon-Meniel, B. / De Sousa, R.A. / Bourg, S. / Figadere, B. / Wolff, N. / Munier-Lehmann, H. / Caillet-Saguy, C.
History
DepositionDec 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tight junction protein ZO-1
B: Tight junction protein ZO-1
C: Envelope small membrane protein
D: Envelope small membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9879
Polymers21,3524
Non-polymers6355
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-47 kcal/mol
Surface area10060 Å2
Unit cell
Length a, b, c (Å)30.127, 76.157, 76.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tight junction protein ZO-1 / Tight junction protein 1 / Zona occludens protein 1 / Zonula occludens protein 1


Mass: 9348.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TJP1, ZO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07157
#2: Protein/peptide Envelope small membrane protein / E / sM protein


Mass: 1327.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: E, 4 / Production host: synthetic construct (others) / References: UniProt: P0DTC4
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 20 %w/v PEG 3350 0.2 M NH4I

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.72→54.12 Å / Num. obs: 25335 / % possible obs: 69.92 % / Redundancy: 13.2 % / Biso Wilson estimate: 29.86 Å2 / CC1/2: 0.998 / Net I/σ(I): 0.846
Reflection shellResolution: 1.721→1.918 Å / Num. unique obs: 684 / CC1/2: 0.617

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→54.12 Å / SU ML: 0.2504 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 39.0706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2727 1316 5.19 %
Rwork0.203 24019 -
obs0.2067 25335 69.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.02 Å2
Refinement stepCycle: LAST / Resolution: 1.72→54.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 5 91 1492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631404
X-RAY DIFFRACTIONf_angle_d0.82021889
X-RAY DIFFRACTIONf_chiral_restr0.0562231
X-RAY DIFFRACTIONf_plane_restr0.0067240
X-RAY DIFFRACTIONf_dihedral_angle_d15.8313529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.790.586100.4132128X-RAY DIFFRACTION3.46
1.79-1.870.4775270.343606X-RAY DIFFRACTION15.69
1.87-1.970.3411620.30361337X-RAY DIFFRACTION35.05
1.97-2.090.32631470.28652997X-RAY DIFFRACTION78.82
2.09-2.260.31592080.26223782X-RAY DIFFRACTION98.62
2.26-2.480.27462210.25163796X-RAY DIFFRACTION99.31
2.48-2.840.33381950.23533782X-RAY DIFFRACTION99.28
2.84-3.580.26192310.19073784X-RAY DIFFRACTION99.78
3.58-54.120.23672150.15523807X-RAY DIFFRACTION99.78
Refinement TLS params.

Method: refined / 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)
10.8125787487571.89820016699-1.580297109054.77771674783-4.605102611727.76706917377-0.05074798686650.1644123261450.135627474393-0.844093035537-0.306408275714-0.9710642745480.1666996417230.6018672801230.03354534045780.32418484526-0.01619326134030.1417757935360.2725875504290.06538537208220.3775294702455.362124712345.13117906085-1.46777591416
27.690735972671.25048762684-5.534395404754.282777298280.4009076880864.37713371656-0.3138518822580.7985928303390.580621759193-0.5065095918860.3357458606310.907200795452-0.0672045865087-0.548774058269-0.1209725039380.1516257747010.0053755661444-0.04397983753460.2203439085540.02378106738860.315452555656-13.7380736086-8.3382832785915.7377005293
38.539611112966.524200236052.578835675865.172909108651.959248706230.7828130514920.2120715941970.002742585720540.4934837934191.303929655560.2675007006531.139600596220.90992598198-2.15014576554-0.3303663198150.418271250315-0.07868177364860.1390607334580.566716394489-0.003004422062540.315301200593-22.0744333974-15.689331574524.4181410762
42.41303654511-0.761136122816-2.527693526094.931669447040.9495924410099.20913085064-0.043267045749-0.5895225022570.0364172919070.620357925592-0.0135868717188-0.0701517570280.2570016734150.110969836263-0.006967408026950.285198961936-0.0386823112459-0.008575909716670.317557597545-0.029086532110.269203325368-9.53278970186-11.583306028321.9876939843
56.349388617743.12356733271-0.6645450008012.491574492810.3489234320593.10901593337-0.2932386159190.623436182028-0.63666752907-0.01158354237130.643315972221-0.2355579103710.4477277661280.3742432094410.1271205961560.2989847050210.06816737464270.009683270007490.1778565170070.0008197676693720.201780799453-1.80942597012-16.005646972812.4343804994
62.596282523752.91686139537-3.252472713794.74531878326-5.32416972125.963058035560.1247238448590.322468336008-0.650604733027-0.868553788283-0.634022822762-0.924472792241.20558609690.01074434811150.4834971422470.441438747779-0.006429246730380.08906948899090.320540581343-0.01085457956430.373885599583-9.1302761555-20.75382874248.7718449401
76.630628494732.649612109162.720618972392.21984931043.616871829956.23560802587-0.118506203184-0.2908532042720.4167968926230.730497716244-0.397871741850.933987814967-0.02434516097990.262112264850.4977295060220.326697542155-0.003519627900610.01285309656130.24605515892-0.01827289740710.266067621846-8.17807858348-14.084073278721.7532998185
87.279781861283.0168854213-0.5716450347483.48071594944-2.036875176445.96531916246-0.313516660251-0.156483313522-0.152916702521-0.1015149710790.2136415735990.3964466046370.54081794054-0.718669403999-0.02769924159920.295391686916-0.04332492357890.0243056774710.184218468978-0.01615821777510.300484167946-17.0739368537-19.356532943619.3187489829
93.795201044190.3379558276290.2128545586055.80759426605-1.44951665225.02334167773-0.09818077413630.2923813263940.35584758081-0.00722980790642-0.0677733252215-0.348835394286-0.3224891309680.0798191473477-0.00953709491310.207618622664-0.004816145008510.009263764343580.1782690598750.03403818187130.227156042394-0.1062261191361.403842015543.34319542001
105.659843675332.65213430044-4.830038734285.54352096194-1.21303330197.948755284050.1027577374290.02008428322650.09475192443660.5734503816210.211568951320.00640306194961-0.948239997111-0.235679989806-0.2687739420320.3452752698520.09497987912880.03082378231990.2177886536340.01907257343230.301769937116-3.037937682596.204682153325.89650488798
110.410416599648-0.544584438601-1.508890763990.8520354773772.193060971895.67188412288-0.1308677840951.219883748321.26935488275-0.4537647633060.5227609910430.503287567543-1.259451612750.109517729533-0.1540198815750.414952130388-0.197658089449-0.08007667384610.696776576480.2796899334180.505584292964-16.1844080262-9.93217098535.27159665863
125.561437543850.8110107837661.775263296015.373555951934.955965919134.760927919480.0296012905686-0.309266551081-0.3835420749820.844917731358-0.226998855178-0.1533756328230.7837993505950.9931799663520.3543582835920.3971724203830.1067779448260.1155563096720.3904710302870.08566278905240.4020203763575.8636137268-10.13785568395.35795744382
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 184 through 203 )AA184 - 2031 - 20
22chain 'A' and (resid 204 through 213 )AA204 - 21321 - 30
33chain 'A' and (resid 214 through 219 )AA214 - 21931 - 36
44chain 'A' and (resid 220 through 232 )AA220 - 23237 - 49
55chain 'A' and (resid 233 through 241 )AA233 - 24150 - 58
66chain 'A' and (resid 242 through 251 )AA242 - 25159 - 68
77chain 'A' and (resid 252 through 266 )AA252 - 26669 - 83
88chain 'B' and (resid 184 through 203 )BB184 - 2031 - 20
99chain 'B' and (resid 204 through 251 )BB204 - 25121 - 68
1010chain 'B' and (resid 252 through 266 )BB252 - 26669 - 83
1111chain 'C' and (resid 1 through 9 )CC1 - 91 - 9
1212chain 'D' and (resid 2 through 9 )DD2 - 91 - 8

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