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

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Basic information

Entry
Database: PDB / ID: 4joe
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide A-iCAL36 (ANSRAPTSII)
Components
  • A-iCAL36 peptide
  • Golgi-associated PDZ and coiled-coil motif-containing protein
KeywordsPEPTIDE BINDING PROTEIN / PDZ / CFTR Associated Ligand / CAL / FIG / PIST
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 / trans-Golgi network transport vesicle / 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 / Golgi-associated vesicle membrane / trans-Golgi network transport vesicle / 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: 1.14 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
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: A-iCAL36 peptide
D: A-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9526
Polymers20,7684
Non-polymers1842
Water4,234235
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: A-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5684
Polymers10,3842
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-5 kcal/mol
Surface area5460 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: A-iCAL36 peptide


Theoretical massNumber of molelcules
Total (without water)10,3842
Polymers10,3842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-5 kcal/mol
Surface area5370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.679, 47.816, 97.665
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


Mass: 9353.722 Da / Num. of mol.: 2 / Fragment: CAL 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 A-iCAL36 peptide


Mass: 1030.157 Da / Num. of mol.: 2 / Source method: obtained synthetically
#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.: 235 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 31% (w/v) polyethylene glycol (PEG) 3350, 0.05 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: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 27, 2010
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→18.53 Å / Num. all: 63391 / Num. obs: 63014 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.99 / Rmerge(I) obs: 0.098 / Rsym value: 0.116 / Net I/σ(I): 10.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.14-1.190.3783.9988880.393199.9
1.2-1.280.2485.55104790.3171100
1.29-1.380.1657.2786700.2281100
1.39-1.510.1139.4981720.168199.9
1.52-1.690.07712.1476040.131100
1.7-1.950.05814.6166660.1111100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)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: 1.14→18.53 Å / SU ML: 0.14 / Cross valid method: Omit map / σ(F): 2 / Phase error: 15.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 3144 4.99 %In thin shells
Rwork0.1818 ---
obs0.1846 63011 99.41 %-
all-63014 --
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.097 Å2 / ksol: 0.534 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2941 Å2-0 Å2-0 Å2
2---1.1152 Å2-0 Å2
3----1.1789 Å2
Refinement stepCycle: LAST / Resolution: 1.14→18.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 12 235 1707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051543
X-RAY DIFFRACTIONf_angle_d1.0772090
X-RAY DIFFRACTIONf_dihedral_angle_d13.946587
X-RAY DIFFRACTIONf_chiral_restr0.067241
X-RAY DIFFRACTIONf_plane_restr0.006278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.18140.22963160.23515916X-RAY DIFFRACTION100
1.1814-1.22870.20613160.20715907X-RAY DIFFRACTION100
1.2287-1.28460.20953160.19475947X-RAY DIFFRACTION100
1.2846-1.35240.19883160.18055964X-RAY DIFFRACTION100
1.3524-1.43710.19223160.1695966X-RAY DIFFRACTION100
1.4371-1.5480.18243160.16195983X-RAY DIFFRACTION100
1.548-1.70360.19833160.15845999X-RAY DIFFRACTION100
1.7036-1.94990.19183160.16446052X-RAY DIFFRACTION100
1.9499-2.45580.19163160.17346098X-RAY DIFFRACTION100
2.4558-18.53320.18113000.1956035X-RAY DIFFRACTION95
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)
10.4859-0.3479-0.06580.81240.10390.8186-0.0106-0.0328-0.02420.03450.013-0.01360.01560.0163-0.00030.0404-0.00110.00130.04580.00470.052322.134628.428134.7262
20.5099-0.1786-0.52591.2630.63011.32190.06370.02680.0338-0.2083-0.02570.019-0.18430.0104-0.02420.07780.00520.00540.0480.00290.043925.896126.773910.4696
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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