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- PDB-7ntj: PALS1 PDZ1 domain with SARS-CoV-1_E PBM complex -

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Basic information

Entry
Database: PDB / ID: 7ntj
TitlePALS1 PDZ1 domain with SARS-CoV-1_E PBM complex
Components
  • Envelope small membrane protein
  • MAGUK p55 subfamily member 5
KeywordsCELL ADHESION / cell polarity / PALS1 / SARS-CoV-1
Function / homology
Function and homology information


protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / viral budding from Golgi membrane / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / Tight junction interactions / disruption of plasma membrane integrity in another organism / SARS-CoV-2 targets PDZ proteins in cell-cell junction / lateral loop ...protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / viral budding from Golgi membrane / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / Tight junction interactions / disruption of plasma membrane integrity in another organism / SARS-CoV-2 targets PDZ proteins in cell-cell junction / lateral loop / myelin sheath adaxonal region / regulation of transforming growth factor beta receptor signaling pathway / Translation of Structural Proteins / Virion Assembly and Release / SARS-CoV-1-mediated effects on programmed cell death / Schmidt-Lanterman incisure / peripheral nervous system myelin maintenance / establishment or maintenance of epithelial cell apical/basal polarity / apical junction complex / generation of neurons / central nervous system neuron development / host cell Golgi membrane / bicellular tight junction / Maturation of protein E / Attachment and Entry / endoplasmic reticulum-Golgi intermediate compartment membrane / protein localization to plasma membrane / adherens junction / cerebral cortex development / SARS-CoV-1 activates/modulates innate immune responses / gene expression / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / perikaryon / apical plasma membrane / protein domain specific binding / axon / virion membrane / Golgi apparatus / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
L27-N / MPP5, SH3 domain / L27_N / 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. / L27 domain, C-terminal / L27 domain ...L27-N / MPP5, SH3 domain / L27_N / 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. / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Envelope small membrane protein / Protein PALS1
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsJavorsky, A. / Kvansakul, M.
CitationJournal: Commun Biol / Year: 2021
Title: Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain.
Authors: Javorsky, A. / Humbert, P.O. / Kvansakul, M.
History
DepositionMar 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: MAGUK p55 subfamily member 5
G: Envelope small membrane protein
A: MAGUK p55 subfamily member 5
C: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)20,4654
Polymers20,4654
Non-polymers00
Water5,549308
1
B: MAGUK p55 subfamily member 5
G: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)10,2332
Polymers10,2332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-6 kcal/mol
Surface area5140 Å2
MethodPISA
2
A: MAGUK p55 subfamily member 5
C: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)10,2332
Polymers10,2332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-6 kcal/mol
Surface area5810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.151, 39.963, 40.832
Angle α, β, γ (deg.)94.897, 108.777, 100.842
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein MAGUK p55 subfamily member 5


Mass: 9391.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPP5, PALS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon+ / References: UniProt: Q8N3R9
#2: Protein/peptide Envelope small membrane protein / E protein / sM protein


Mass: 840.961 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus
References: UniProt: P59637
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris pH6.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.74→38.76 Å / Num. obs: 16270 / % possible obs: 96.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.9
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.15 / Num. unique obs: 853 / CC1/2: 0.965 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASER1.18.2_3874+SVNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UU6

4uu6


Resolution: 1.74→38.76 Å / SU ML: 0.1416 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 20.9127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1852 773 4.75 %
Rwork0.1517 15496 -
obs0.1533 16269 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.93 Å2
Refinement stepCycle: LAST / Resolution: 1.74→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 0 308 1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781389
X-RAY DIFFRACTIONf_angle_d0.83931871
X-RAY DIFFRACTIONf_chiral_restr0.0622229
X-RAY DIFFRACTIONf_plane_restr0.0045242
X-RAY DIFFRACTIONf_dihedral_angle_d27.1265529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.850.22311080.17312541X-RAY DIFFRACTION93.8
1.85-1.990.20181290.15812571X-RAY DIFFRACTION96.19
1.99-2.190.19191350.1432580X-RAY DIFFRACTION96.45
2.19-2.50.18761180.14352620X-RAY DIFFRACTION97.3
2.5-3.150.21111360.15742588X-RAY DIFFRACTION96.77
3.15-38.760.16041470.14942596X-RAY DIFFRACTION97.65
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)
11.04832478548-0.4295792954810.1039230397943.5874158265-1.233475751132.238063539750.096328903267-0.157306384081-0.1847973571450.4009306346580.140153455268-0.0183529483772-0.0416421950271-0.05034542318480.01245102984160.151647762473-0.00225973715291-0.01196257417390.1186812969480.01203240553880.15734691900623.2875591362-14.4620743857-8.13717190643
25.40581449641-0.05495119984674.236070560462.26874166865-2.366973438765.963031667720.0224905653407-0.02926476890850.3716972962460.325534082977-0.115878937850.111283741843-0.476783359244-0.2748964066950.02838082055850.1281622970960.008726528910950.05284656634230.1524319467010.04176858343650.12309327366218.5284150396-2.25712827891-19.9334846211
33.615263194164.08363852001-2.228997676925.69234582093-3.98927290074.27511688641-0.0268017745464-0.210818379223-0.564468046278-0.272278187281-0.229621622159-0.4207010337190.324622637443-0.07314180125260.1005060480910.119102539321-0.0207913838461-0.003900994849520.124458116442-0.01134603158560.16980730447312.9726224919-21.8559059471-19.4357105791
44.104006542641.6069327272-2.084065685632.20311585382-0.7893978910812.645801124420.2080915471940.00644435945464-0.455256123085-0.0997995778979-0.276615714164-0.1556495448510.05657996803010.07901684971230.0544832905920.1374985582370.02936450402350.008572361602960.130886856663-0.0006320679772430.15439800365618.6680088038-19.5399901219-20.8361269118
56.386309117591.115928895895.442135887775.39459842657-0.3571687484128.28553981920.1090185621090.225760082388-0.0681529862478-0.498678173772-0.120931309967-0.21761178532-0.04821426543030.611862328137-0.1278086105720.1446466452790.02067723242720.03800539223990.1560500095140.01642806671120.12584073692128.1547230279-9.94672585807-23.967680914
61.920289169320.0600096247818-0.08226759730141.807496178620.5733652668361.16024889825-0.0329596955407-0.0453390196539-0.1840808459050.03923079380330.075347261746-0.02083882821560.05384270015370.07494505184540.004186872864970.1354843738230.01540888716840.004524464250520.1384428226940.01441283506020.11086958256421.5541088615-17.8059160788-14.1989410581
72.420104475542.040844051850.7171207654494.16705506112.55106733192.234372249160.157231643316-0.338244734881-0.2184351420210.2797972219240.00184894230132-0.02060317306030.299209899676-0.293718939640.1017404310660.1809128849360.01141276792870.005926153604320.1683644235220.02893748892260.13361448410210.7899758948-15.9507255762-9.27635971744
84.272173451092.290095630130.1214192727345.2741659458-1.072316700221.30159067595-0.0548627557469-0.07177604091450.2603597790440.144598369362-0.0579475749211-0.128986624666-0.1520321519170.1015414877680.05847850047390.105779128880.01556485838930.00433130486820.1397169782030.001848634075450.1198820568689.68511774009-8.80636119023-16.3550312976
91.61431081731-0.03544315687560.192805599734.4517878655-0.6560579301242.122343624850.05935050624520.0337896752639-0.0777614206570.379924131799-0.08758660696720.001931529321470.06869783083280.19835341339-0.02734223380310.1229846540760.0127204645820.00716515795430.14978673820.01814192854160.15020300309220.5524517868-11.9288423887-10.383229805
102.24360463461-0.53054495607-0.3725625429744.39967547101-1.676451523160.834949516582-0.09974553696590.21177175622-0.514874465552-0.323614316968-0.2802408390970.2378169828420.0715291134268-0.1438237061120.004540846156530.182111778807-0.003207484456270.03964417434530.156474432843-0.0291065718690.14653231792514.8072257504-12.9817169728-24.1254522026
113.217358444620.642414172866-0.3985060507921.66574592435-0.1441712625072.933649480560.1088366139930.1360334487030.165066376836-0.19195740926-0.110425025251-0.2650047436090.01291019826340.0217062675079-0.02009108922420.1057370150470.02146431907360.02036353900130.177549878260.04058062586720.1609183600619.83318391432.203230484560.713445028582
122.348463322940.538650563339-1.401376968956.44797614239-3.920762355462.88920392194-0.1135693029360.1389213826750.0175934255058-0.1473545789770.349324112820.1342456737810.484847407654-0.2091996449530.07779004203630.195445697676-0.0519057575622-0.009485100717720.1415313040170.02803361983280.1065035571828.9274872642-10.47402557357.91288387402
133.75135014396-0.2832136390231.317338669462.334868721-0.4849367909217.81293973119-0.149250367213-0.08652836472360.1313887197550.133138327945-0.0236075295736-0.0387072433095-0.591537282269-0.1486510277550.02565887632950.1549160863340.01000903636795.20995851849E-50.11975695563-0.005914185481750.1334763382345.669117477187.533303374165.51307204173
143.51513771510.630821110707-5.09090637696.233178567130.6339907090567.80163417916-0.0167249210735-0.399473883663-0.1478468173730.5252402504320.0674102220943-0.1397642288790.5802929015780.1152106933470.02971271507890.160772848464-0.00751159252084-0.04380215739040.1579595214790.005162374468320.11732001685713.6394240613-2.1577599523516.7145006661
151.77433245908-0.223534994221-0.06531519820941.51219349110.383697970531.515231033490.006195580840650.02982708733940.1336275311090.001222110898490.0450410086833-0.00357361591870.01725260926620.0166927311812-0.03275280246840.1190202208890.004486446746780.01547017339180.1208919415270.01788358613290.13788474090911.70505475244.320699661720.0809952886863
162.54879497380.214812550131-0.7752645231531.52075644302-0.08193541992961.30531937809-0.01596966151570.145813856562-0.06889808223910.01372837725110.00634292260627-0.04378246367720.0396071655854-0.008489216263160.00991474211310.1285054398070.005669759587830.001721656119930.1351300255290.008830650961760.096660325099810.3787675551-2.318095969220.4307492989
172.377133988481.47730190187-1.685458394782.656770890341.058596511936.08362647858-0.0061968384842-0.3262246704560.457930427145-0.378078096127-0.1493508766130.535164055494-0.183534039003-0.5349308601890.008279827719640.124737891733-0.00679527873165-0.04034030326080.192135052527-0.05655654142860.2457583108660.1158138839372.527978945218.49944709046
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 250 through 261 )BA250 - 2611 - 12
22chain 'B' and (resid 262 through 268 )BA262 - 26813 - 19
33chain 'B' and (resid 269 through 276 )BA269 - 27620 - 27
44chain 'B' and (resid 277 through 283 )BA277 - 28328 - 34
55chain 'B' and (resid 284 through 292 )BA284 - 29235 - 43
66chain 'B' and (resid 293 through 304 )BA293 - 30444 - 55
77chain 'B' and (resid 305 through 313 )BA305 - 31356 - 64
88chain 'B' and (resid 314 through 323 )BA314 - 32365 - 74
99chain 'B' and (resid 324 through 335 )BA324 - 33575 - 86
1010chain 'G' and (resid 208 through 211 )GB208 - 2111 - 4
1111chain 'A' and (resid 250 through 261 )AC250 - 2611 - 12
1212chain 'A' and (resid 262 through 268 )AC262 - 26813 - 19
1313chain 'A' and (resid 269 through 283 )AC269 - 28320 - 34
1414chain 'A' and (resid 284 through 292 )AC284 - 29235 - 43
1515chain 'A' and (resid 293 through 313 )AC293 - 31344 - 64
1616chain 'A' and (resid 314 through 335 )AC314 - 33565 - 86
1717chain 'C' and (resid 205 through 211 )CD205 - 2111 - 7

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