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- PDB-7jzo: CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic L... -

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Basic information

Entry
Database: PDB / ID: 7jzo
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALTPP
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • LyCALTPP peptide core
KeywordsPEPTIDE BINDING PROTEIN / PDZ domain / inhibitor / complex / peptidomimetic
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 / lysosomal membrane / Golgi 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
3-(thiophen-2-yl)propanoic acid / 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: 1.61 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 LyCALTPP
Authors: Gill, N.P.
History
DepositionSep 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Golgi-associated PDZ and coiled-coil motif-containing protein
B: Golgi-associated PDZ and coiled-coil motif-containing protein
C: LyCALTPP peptide core
D: LyCALTPP peptide core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3818
Polymers20,8844
Non-polymers4974
Water3,441191
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: LyCALTPP peptide core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7825
Polymers10,4422
Non-polymers3403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-6 kcal/mol
Surface area5550 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: LyCALTPP peptide core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5983
Polymers10,4422
Non-polymers1561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-5 kcal/mol
Surface area5120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.804, 47.812, 97.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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 LyCALTPP peptide core


Mass: 1088.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-QTU / 3-(thiophen-2-yl)propanoic acid


Mass: 156.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 41.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 5.36 mg/mL CAL PDZ, 1 mM LyCALTPP, 31% (w/v) PEG 8000, 150 mM NaCl, 100 mM Tris pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792909 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792909 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 22749 / % possible obs: 98.4 % / Redundancy: 9.17 % / Biso Wilson estimate: 13.31 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.132 / Net I/σ(I): 15.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
8-105.750.06818.48890.9920.07880.9
6-87.590.0820.192660.9890.08894.3
5-68.620.07822.163470.9870.08498
4.79-57.940.08121.261090.9870.08896.5
3.4-4.798.90.08522.4416110.9880.09198.2
2.78-3.49.960.122.0720710.9910.106100
2.15-2.7810.20.14120.2852080.990.15100
1.96-2.1510.40.18217.6930850.9850.193100
1.82-1.9610.20.20614.1931440.9870.218100
1.7-1.829.760.23910.6935780.9830.254100
1.61-1.74.60.2915.4631720.9360.32693.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDSVersion November 1, 2016data reduction
XSCALEVersion November 1, 2016data scaling
PHENIX1.17.1-3660phasing
PHENIX1.17.1-3660model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NMO

4nmo


Resolution: 1.61→48.96 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 1139 5.01 %
Rwork0.175 21611 -
obs0.1765 22749 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.05 Å2 / Biso mean: 17.1044 Å2 / Biso min: 5.69 Å2
Refinement stepCycle: final / Resolution: 1.61→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 12 191 1640
Biso mean--27.61 26.58 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071478
X-RAY DIFFRACTIONf_angle_d0.9491989
X-RAY DIFFRACTIONf_dihedral_angle_d24.54559
X-RAY DIFFRACTIONf_chiral_restr0.065231
X-RAY DIFFRACTIONf_plane_restr0.006255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.61-1.680.30611140.21882408252289
1.68-1.770.2441710.194326822853100
1.77-1.880.23261130.183627192832100
1.88-2.030.17851710.15926892860100
2.03-2.230.17671140.171227732887100
2.23-2.550.23331710.178127252896100
2.55-3.210.19891140.177828262940100
3.22-48.960.18721710.16572789296096

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