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- PDB-4k72: CFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36-V... -

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Basic information

Entry
Database: PDB / ID: 4k72
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36-VQD (ANSRVQDSII)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36-VQD peptide
KeywordsPEPTIDE BINDING PROTEIN/PROTEIN BINDING / PDZ domain / CAL / PIST / FIG / PDZ-peptide complex / CFTR Associated Ligand / CFTR / PEPTIDE BINDING PROTEIN-PROTEIN BINDING 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 / trans-Golgi network transport vesicle / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / apical protein localization / RHOQ GTPase cycle / molecular sequestering activity / 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 / trans-Golgi network transport vesicle / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / apical protein localization / RHOQ GTPase cycle / molecular sequestering activity / 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
Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: Structure / Year: 2014
Title: Stereochemical Preferences Modulate Affinity and Selectivity among Five PDZ Domains that Bind CFTR: Comparative Structural and Sequence Analyses.
Authors: Amacher, J.F. / Cushing, P.R. / Brooks, L. / Boisguerin, P. / Madden, D.R.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all ..._reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.2Sep 20, 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

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-VQD peptide
D: iCAL36-VQD peptide


Theoretical massNumber of molelcules
Total (without water)20,9144
Polymers20,9144
Non-polymers00
Water2,540141
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36-VQD peptide


Theoretical massNumber of molelcules
Total (without water)10,4572
Polymers10,4572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-3 kcal/mol
Surface area4890 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: iCAL36-VQD peptide


Theoretical massNumber of molelcules
Total (without water)10,4572
Polymers10,4572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-3 kcal/mol
Surface area5420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.250, 48.791, 54.900
Angle α, β, γ (deg.)90.00, 92.79, 90.00
Int Tables number4
Space group name H-MP1211

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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: PDZ domain
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-VQD peptide


Mass: 1103.208 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40% (w/v) polyethylene glycol (PEG) 1000, 0.1 M sodium thiosulfate pentahydrate, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 8.0, 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 27, 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: 1.9→19.57 Å / Num. all: 15231 / Num. obs: 15168 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.59 / Rmerge(I) obs: 0.128 / Rsym value: 0.065 / Net I/σ(I): 15.58
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRsym valueDiffraction-ID% possible all
1.9-2.030.5143.5928920.36199.5
2.04-2.190.2885.9124420.219199.6
2.2-2.40.1928.423320.149199.7
2.41-2.680.13111.8521000.102199.8
2.69-3.080.07618.418270.061199.9
3.09-3.760.03331.0216040.034199.8

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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 (CAL PDZ domain bound to iCAL36 peptide)

4e34


Resolution: 1.9→19.57 Å / SU ML: 0.28 / Cross valid method: Omit map / σ(F): 2 / σ(I): 3.59 / Phase error: 22.09 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 763 5.03 %In thin shells
Rwork0.1785 ---
obs0.1808 15162 99.66 %-
all-15168 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.589 Å2 / ksol: 0.417 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6196 Å20 Å2-0.8544 Å2
2--3.9701 Å2-0 Å2
3----6.5896 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 0 141 1558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071444
X-RAY DIFFRACTIONf_angle_d1.0961949
X-RAY DIFFRACTIONf_dihedral_angle_d15.44543
X-RAY DIFFRACTIONf_chiral_restr0.067229
X-RAY DIFFRACTIONf_plane_restr0.005256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.04660.26151470.20772836X-RAY DIFFRACTION99
2.0466-2.25230.24851490.17922880X-RAY DIFFRACTION100
2.2523-2.57750.25611490.1832869X-RAY DIFFRACTION100
2.5775-3.2450.25311620.17752878X-RAY DIFFRACTION100
3.245-19.57070.18721560.16992936X-RAY DIFFRACTION100
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)
10.59050.0483-0.45380.82660.06060.7055-0.004-0.08320.01380.05170.00140.0153-0.09370.0434-0.00840.1135-0.003-0.00370.1203-0.00360.11227.472827.408340.0222
21.00080.4209-0.24350.5627-0.40670.96650.0367-0.0243-0.0316-0.038-0.01560.00890.13010.1296-0.02390.12540.0199-0.0070.1066-0.01750.133315.084129.306817.1063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 284:370
2X-RAY DIFFRACTION2CHAIN B AND RESID 284:370

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