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- PDB-6v84: CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic L... -

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Basic information

Entry
Database: PDB / ID: 6v84
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALAc
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • LyCALAc
KeywordsPEPTIDE BINDING PROTEIN/INHIBITOR / PDZ domain / Inhibitor / Complex / Peptidomimetic / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


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 / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport ...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 / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / transmembrane transporter binding / postsynaptic density / Golgi membrane / lysosomal membrane / dendrite / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
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
Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGill, N.P. / Madden, D.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK101541 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008704 United States
CitationJournal: To Be Published
Title: CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALAc
Authors: Gill, N.P.
History
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
C: LyCALAc
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: LyCALAc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4269
Polymers20,9664
Non-polymers4605
Water4,035224
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: LyCALAc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7595
Polymers10,4832
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area5620 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: LyCALAc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6674
Polymers10,4832
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-7 kcal/mol
Surface area5200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.568, 47.741, 97.448
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 Golgi-associated PDZ and coiled-coil motif-containing protein / CFTR-associated ligand / Fused in glioblastoma / PDZ protein interacting specifically with TC10 / PIST


Mass: 9353.722 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9HD26
#2: Protein/peptide LyCALAc


Mass: 1129.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Engineered / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5.5 mg/mL CAL PDZ, 1 mM LyCALAc peptide, 35% (w/v) PEG 8000, 150 mM NaCl, 100 mM Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.8263 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2017
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8263 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 20936 / % possible obs: 96.8 % / Redundancy: 5.59 % / Biso Wilson estimate: 14.19 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.105 / Net I/σ(I): 14.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
7-105.330.05225.262050.9970.05898.1
5-75.480.06223.565120.9940.06997.3
4.62-55.410.0625.952010.9960.06793.5
3.28-4.625.440.06624.3217450.9930.07496.7
2.68-3.285.950.08821.6822490.9920.09798.4
2.32-2.685.940.11218.0626410.990.12398.4
2.08-2.325.630.11515.4428860.990.12798.6
1.9-2.085.910.1513.0731990.9850.16597.8
1.75-1.95.990.228.9637300.9720.24297.7
1.64-1.754.490.2985.3734600.9440.33691.8

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Processing

Software
NameVersionClassification
XDSVersion Novermber 1, 2016data reduction
XSCALEVersion Novermber 1, 2016data scaling
PHENIXv1.17.1-3660phasing
PHENIXv1.17.1-3660model building
PHENIXv1.17.1-3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NMO

4nmo


Resolution: 1.64→34.24 Å / SU ML: 0.1863 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.6707
RfactorNum. reflection% reflection
Rfree0.2131 1060 5.07 %
Rwork0.1797 --
obs0.1813 20925 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.37 Å2
Refinement stepCycle: LAST / Resolution: 1.64→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 30 224 1685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111505
X-RAY DIFFRACTIONf_angle_d1.3042032
X-RAY DIFFRACTIONf_chiral_restr0.0865236
X-RAY DIFFRACTIONf_plane_restr0.0083265
X-RAY DIFFRACTIONf_dihedral_angle_d24.8789576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.710.38331060.28212307X-RAY DIFFRACTION90.54
1.71-1.810.22111590.21172383X-RAY DIFFRACTION96.58
1.81-1.920.21581060.18772494X-RAY DIFFRACTION97.31
1.92-2.070.20021590.17682454X-RAY DIFFRACTION97.94
2.07-2.270.1951060.16822538X-RAY DIFFRACTION98.11
2.27-2.60.2371590.18512504X-RAY DIFFRACTION98.81
2.6-3.280.19741060.17392573X-RAY DIFFRACTION98.17
3.28-34.240.19741590.16392612X-RAY DIFFRACTION96.42

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