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- PDB-4nmo: CFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(A... -

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Basic information

Entry
Database: PDB / ID: 4nmo
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(Ac-K-1)(ANSRWPTS[Ac-K]I)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36(Ac-K-1) peptide
Keywordsprotein transport/inhibitor / PDZ domain / CAL / FIG / PIST / GOPC / PDZ-peptide complex / CFTR / CFTR Associated Ligand / protein transport / protein transport-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 / trans-Golgi network transport vesicle / apical protein localization / molecular sequestering activity / 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 / trans-Golgi network transport vesicle / apical protein localization / molecular sequestering activity / 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 / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
iCAL36(Ac-K-1) peptide / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: Plos One / Year: 2014
Title: Chemically Modified Peptide Scaffolds Target the CFTR-Associated Ligand PDZ Domain.
Authors: Amacher, J.F. / Zhao, R. / Spaller, M.R. / Madden, D.R.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 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
B: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(Ac-K-1) peptide
D: iCAL36(Ac-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2966
Polymers21,1124
Non-polymers1842
Water3,657203
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(Ac-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6483
Polymers10,5562
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area5440 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: iCAL36(Ac-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6483
Polymers10,5562
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6 kcal/mol
Surface area5380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.083, 47.603, 97.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Fragment: UNP RESIDUES 284-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9HD26
#2: Protein/peptide iCAL36(Ac-K-1) peptide


Type: Oligopeptide / Class: Inhibitor / Mass: 1202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: iCAL36(Ac-K-1) peptide
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 27% (w/v) polyethylene glycol (PEG), 0.15 M sodium chloride, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 18, 2011
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.4→19.5 Å / Num. all: 34123 / Num. obs: 34205 / % possible obs: 99.8 % / Observed criterion σ(F): 7.2 / Observed criterion σ(I): 30.16 / Rsym value: 0.072 / Net I/σ(I): 30.16
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.4-1.524.83785055.7199.2
1.53-1.648.9525034199.8
1.65-1.814.75501621.21100
1.81-2.0127.01441511.31100
2.02-2.3243.5538736.51100
2.33-2.8356.9934674.41100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E34

4e34


Resolution: 1.4→19.471 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 17.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 1716 5.03 %In thin shells
Rwork0.1834 ---
obs0.1844 34123 99.02 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.986 Å2 / ksol: 0.441 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.7918 Å2-0 Å2-0 Å2
2---1.3497 Å2-0 Å2
3----1.3683 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 12 203 1680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121531
X-RAY DIFFRACTIONf_angle_d1.2212069
X-RAY DIFFRACTIONf_dihedral_angle_d14.341577
X-RAY DIFFRACTIONf_chiral_restr0.067235
X-RAY DIFFRACTIONf_plane_restr0.012268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3935-1.43450.30891210.26832379X-RAY DIFFRACTION89
1.4345-1.48080.2441340.24132658X-RAY DIFFRACTION99
1.4808-1.53370.22141710.21252691X-RAY DIFFRACTION100
1.5337-1.59510.23361100.18772686X-RAY DIFFRACTION100
1.5951-1.66760.21721480.17762689X-RAY DIFFRACTION100
1.6676-1.75550.20421720.17932687X-RAY DIFFRACTION100
1.7555-1.86540.1997940.17172743X-RAY DIFFRACTION100
1.8654-2.00930.18111640.16352715X-RAY DIFFRACTION100
2.0093-2.21130.19681720.16762696X-RAY DIFFRACTION100
2.2113-2.53060.1621080.18582785X-RAY DIFFRACTION100
2.5306-3.18610.2291500.17952786X-RAY DIFFRACTION100
3.1861-19.47280.18791720.17872892X-RAY DIFFRACTION100

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