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

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Basic information

Entry
Database: PDB / ID: 4nmt
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(TFA-K-1) (ANSRWPTS[Tfa-acyl-K]I)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36(TFA-K-1) peptide
Keywordsprotein transport/inhibitor / CAL / PIST / GOPC / FIG / CFTR / PDZ / PDZ-peptide / 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 / molecular sequestering activity / apical protein localization / 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 / molecular sequestering activity / apical protein localization / 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 / 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(TFA-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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(TFA-K-1) peptide
D: iCAL36(TFA-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4046
Polymers21,2204
Non-polymers1842
Water4,053225
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(TFA-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7023
Polymers10,6102
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-7 kcal/mol
Surface area5320 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: iCAL36(TFA-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7023
Polymers10,6102
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.986, 47.944, 97.454
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(TFA-K-1) peptide


Type: Oligopeptide / Class: Inhibitor / Mass: 1256.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: iCAL36(TFA-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.: 225 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 33% (w/v) polyethylene glycol (PEG), 0.2 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: 34177 / Num. obs: 32898 / % possible obs: 96.3 % / Observed criterion σ(F): 7.6 / Observed criterion σ(I): 17.6
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.4-1.523.7278480.52194.2
1.53-1.646.2852530.329195.5
1.65-1.89.6647240.205196.5
1.81-216.2845460.113196.8
2.01-2.3125.6340190.069197.4
2.32-2.8232.4634140.05197.5

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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→19.5 Å / SU ML: 0.19 / Cross valid method: omit peptide density / σ(F): 1.99 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1636 4.97 %In thin shells
Rwork0.1802 ---
obs0.1811 32898 95.13 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.558 Å2 / ksol: 0.428 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.406 Å20 Å2-0 Å2
2--0.619 Å2-0 Å2
3----0.1476 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1471 0 12 225 1708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081567
X-RAY DIFFRACTIONf_angle_d1.1292128
X-RAY DIFFRACTIONf_dihedral_angle_d14.927593
X-RAY DIFFRACTIONf_chiral_restr0.066238
X-RAY DIFFRACTIONf_plane_restr0.005278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.392-1.43290.2957980.24352130X-RAY DIFFRACTION79
1.4329-1.47920.25171420.23892525X-RAY DIFFRACTION94
1.4792-1.5320.21591630.20972558X-RAY DIFFRACTION95
1.532-1.59330.2356960.1992615X-RAY DIFFRACTION95
1.5933-1.66580.22811520.1862573X-RAY DIFFRACTION96
1.6658-1.75360.21981630.18012571X-RAY DIFFRACTION96
1.7536-1.86340.1791850.1742696X-RAY DIFFRACTION97
1.8634-2.00710.18451580.16052644X-RAY DIFFRACTION97
2.0071-2.20890.18161610.16582632X-RAY DIFFRACTION97
2.2089-2.52790.1748960.17992734X-RAY DIFFRACTION97
2.5279-3.18270.19761590.17642725X-RAY DIFFRACTION98
3.1827-19.54720.18761630.17312859X-RAY DIFFRACTION98

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