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- PDB-4e35: Crystal structure of CFTR Associated Ligand (CAL) PDZ domain boun... -

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Basic information

Entry
Database: PDB / ID: 4.0E+35
TitleCrystal structure of CFTR Associated Ligand (CAL) PDZ domain bound to iCAL36-L (ANSRWPTSIL) peptide
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL50 peptide
KeywordsPROTEIN TRANSPORT/PROTEIN BINDING / PDZ-peptide complex / PROTEIN TRANSPORT-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 / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / molecular sequestering activity / trans-Golgi network transport vesicle / 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 / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / 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 / membrane / identical protein binding / 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: 1.4 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Stereochemical Determinants of C-terminal Specificity in PDZ Peptide-binding Domains: A NOVEL CONTRIBUTION OF THE CARBOXYLATE-BINDING LOOP.
Authors: Amacher, J.F. / Cushing, P.R. / Bahl, C.D. / Beck, T. / Madden, D.R.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Sep 13, 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: iCAL50 peptide
D: iCAL50 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4589
Polymers20,9984
Non-polymers4605
Water3,315184
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL50 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6834
Polymers10,4992
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area5330 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: iCAL50 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7755
Polymers10,4992
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-8 kcal/mol
Surface area5440 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 / CAL / CFTR-associated ligand / Fused in glioblastoma / PDZ protein interacting specifically with TC10 / PIST


Mass: 9353.722 Da / Num. of mol.: 2 / Fragment: PDZ domain (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 iCAL50 peptide


Mass: 1145.289 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% w/v PEG8000, 0.15 M sodium chloride, 0.1 M 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: Apr 5, 2011
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→19.471 Å / Num. all: 34010 / Num. obs: 33518 / % possible obs: 98.61 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.067 / Rsym value: 0.049 / Net I/σ(I): 22.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.4-1.490.3764.2760680.449197.1
1.5-1.610.2037.5155020.248198
1.62-1.760.12112.5749730.144198.4
1.77-1.970.06321.3347570.08199.3
1.98-2.270.03233.4841220.049199.4
2.28-2.780.02340.9336220.038199.7

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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: 0.2 / σ(F): 2 / σ(I): 4 / Phase error: 17.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 1675 5 %IN THIN SHELLS
Rwork0.1842 ---
obs0.1849 33518 98.61 %-
all-34010 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.973 Å2 / ksol: 0.455 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8813 Å2-0 Å2-0 Å2
2---1.7529 Å2-0 Å2
3----0.1284 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 30 184 1673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061518
X-RAY DIFFRACTIONf_angle_d1.1292049
X-RAY DIFFRACTIONf_dihedral_angle_d14.669569
X-RAY DIFFRACTIONf_chiral_restr0.07234
X-RAY DIFFRACTIONf_plane_restr0.006266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.44120.27511620.25562533X-RAY DIFFRACTION97
1.4412-1.48770.2842820.24532619X-RAY DIFFRACTION97
1.4877-1.54090.24981670.21342539X-RAY DIFFRACTION98
1.5409-1.60250.19391650.18712584X-RAY DIFFRACTION98
1.6025-1.67540.1994850.1792660X-RAY DIFFRACTION99
1.6754-1.76370.20111650.1812618X-RAY DIFFRACTION98
1.7637-1.87410.20141210.17522662X-RAY DIFFRACTION99
1.8741-2.01870.19151340.16632669X-RAY DIFFRACTION99
2.0187-2.22160.1861700.17532653X-RAY DIFFRACTION100
2.2216-2.54240.17671330.17872710X-RAY DIFFRACTION100
2.5424-3.20090.18391220.18332766X-RAY DIFFRACTION100
3.2009-19.4710.20021690.18222830X-RAY DIFFRACTION99
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)
10.6565-0.3844-0.10070.50980.18960.4192-0.0686-0.0627-0.06910.08150.04370.05560.03490.015-0.01060.07110.01080.00860.05440.01610.058421.69528.517934.4935
20.6228-0.3425-0.55870.7840.34080.59590.06510.06740.0297-0.1606-0.0192-0.0131-0.09830.00810.00080.0882-0.00480.00440.07550.00350.057725.684826.985410.4802
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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