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- PDB-6xnj: Crystal structure of the PDZ domain of human GOPC in complex with... -

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Basic information

Entry
Database: PDB / ID: 6xnj
TitleCrystal structure of the PDZ domain of human GOPC in complex with a peptide of E. coli O157:H7 str. Sakai effector NleG8
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • NleG8 peptide
KeywordsPROTEIN BINDING / UBIQUITINATION / EFFECTORS / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID
Function / homology
Function and homology information


biological process involved in symbiotic interaction / negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / RHOQ GTPase cycle ...biological process involved in symbiotic interaction / negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-protein transferase activity / protein transport / transmembrane transporter binding / postsynaptic density / lysosomal membrane / Golgi membrane / dendrite / Golgi apparatus / protein-containing complex / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Effector protein NleG / Effector protein NleG superfamily / Effector protein NleG / Golgi-associated PDZ and coiled-coil motif-containing protein / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
T3SS secreted effector NleG / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli O157:H7 str. Sakai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStogios, P.J. / Skarina, T. / Popov, G. / Chang, C. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of the PDZ domain of human GOPC in complex with a peptide of E. coli O157:H7 str. Sakai effector NleG8
Authors: Popov, G.
History
DepositionJul 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Golgi-associated PDZ and coiled-coil motif-containing protein
B: NleG8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0514
Polymers10,8582
Non-polymers1922
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-23 kcal/mol
Surface area5380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.759, 68.759, 59.941
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

21A-530-

HOH

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Components

#1: Protein Golgi-associated PDZ and coiled-coil motif-containing protein / CFTR-associated ligand / Fused in glioblastoma / PDZ protein interacting specifically with TC10 / PIST


Mass: 9725.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Magic / References: UniProt: Q9HD26
#2: Protein/peptide NleG8 peptide


Mass: 1133.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 str. Sakai (bacteria)
Strain: O157:H7 strain Sakai / Gene: NleG8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XAN6*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5 M ammonium sulfate, 15% sucrose, 0.1 M Hepes pH 7.5, 2 mM peptide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→35 Å / Num. obs: 14417 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Net I/σ(I): 18.11
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 723 / CC1/2: 0.967 / Rpim(I) all: 0.283 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+34 / Resolution: 1.85→34.38 Å / SU ML: 0.1754 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.3201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 709 4.92 %RANDOM
Rwork0.1611 13688 --
obs0.1627 14397 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.41 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms723 0 10 169 902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087753
X-RAY DIFFRACTIONf_angle_d0.89131021
X-RAY DIFFRACTIONf_chiral_restr0.0656119
X-RAY DIFFRACTIONf_plane_restr0.0069133
X-RAY DIFFRACTIONf_dihedral_angle_d23.7794286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.990.21251400.19352684X-RAY DIFFRACTION99.3
1.99-2.190.22361440.17422691X-RAY DIFFRACTION99.89
2.19-2.510.21851380.15882729X-RAY DIFFRACTION99.83
2.51-3.160.19211430.17382738X-RAY DIFFRACTION99.79
3.16-34.380.17771440.14622846X-RAY DIFFRACTION99.7
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)
12.26057917684-3.71907356748-2.174798053976.853205344262.566832287898.25136661334-0.0556789039310.1057983081860.1159072579530.1520409473610.03534877178040.192821834999-0.0653847290524-0.363235095249-0.02225430956340.1536018031380.00815123070151-0.00855774284970.09333098272160.003046713069370.15828864937130.7513851726-14.3241843868-22.2140270959
22.847235851240.9973611270810.1719040419252.65552188875-0.4787125642213.244343530810.0589108459409-0.1462772099670.02300521195330.0188632653778-0.088987379718-0.059901774278-0.000476189815462-0.05381589101790.02853690179560.1481011050270.0133584880930.006601484279240.127609742149-0.004094604968860.14603352928936.2007288794-13.3403736648-14.3574999817
33.5956507053-0.2175014509110.3743495205075.712180130621.512505561065.067420842440.08958090163950.007332299756550.114507415247-0.0245406581558-0.111637768722-0.171891050461-0.2643899550440.07043548158120.05242517747270.11995719835-0.02053376580070.04139734671420.1034021560630.03203064176140.12403358865536.5080989553-7.51361323851-17.4900226982
43.898835865283.126115988843.981494274646.378743942450.2108387677416.90601078811-0.0648639474953-0.6254627391640.4000174893980.458055372037-0.09125007482820.217853114168-0.886431623697-0.2498044592280.2200576492670.2959530567610.007801692194780.04863188105790.222687436463-0.03359324596070.21675355861636.1755019745-9.01147594073-4.13086366889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 276:288
2X-RAY DIFFRACTION2chain A and resid 289:337
3X-RAY DIFFRACTION3chain A and resid 338:362
4X-RAY DIFFRACTION4chain B and resid 208:215

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