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

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Basic information

Entry
Database: PDB / ID: 4jof
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide L-iCAL36 (ANSRLPTSII)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • L-iCAL36 peptide
KeywordsPEPTIDE BINDING PROTEIN / PDZ / CFTR Associated Ligand / CAL / PIST / FIG
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 to plasma membrane transport / Golgi-associated vesicle membrane / trans-Golgi network transport vesicle / 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 to plasma membrane transport / Golgi-associated vesicle membrane / trans-Golgi network transport vesicle / 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: 1.2 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 1.1Oct 21, 2020Group: Data collection / Derived calculations / Category: reflns_shell / struct_site
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value ..._reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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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: L-iCAL36 peptide
D: L-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0366
Polymers20,8524
Non-polymers1842
Water4,125229
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: L-iCAL36 peptide


Theoretical massNumber of molelcules
Total (without water)10,4262
Polymers10,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-6 kcal/mol
Surface area5390 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: L-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6104
Polymers10,4262
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8 kcal/mol
Surface area5090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.236, 47.575, 97.291
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 L-iCAL36 peptide


Mass: 1072.237 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.: 229 / 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: 2.01 Å3/Da / Density % sol: 38.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.95
Details: 36% (w/v) polyethylene glycol (PEG)8000, 0.2 M sodium chloride, 0.01 M tris(hydroxymethyl)aminomethane (Tris) hydrochloride (HCl), pH 7.95, 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: Sep 7, 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: 1.2→34.01 Å / Num. all: 53479 / Num. obs: 53402 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4.24 / Rmerge(I) obs: 0.087 / Rsym value: 0.063 / Net I/σ(I): 20.98
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.2-1.240.4194.240.515199.9
1.25-1.340.2945.760.373199.9
1.35-1.470.1818.960.2341100
1.48-1.640.09914.610.1321100
1.65-1.90.05423.460.0731100
1.91-2.320.02440.140.041100

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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: 1.2→34.01 Å / SU ML: 0.14 / Cross valid method: Omit map / σ(F): 2 / Phase error: 17.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 2674 5.01 %In thin shells
Rwork0.1885 ---
obs0.1888 53398 99.85 %-
all-53402 --
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.85 Å2 / ksol: 0.445 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9911 Å2-0 Å2-0 Å2
2---1.1778 Å2-0 Å2
3----0.8133 Å2
Refinement stepCycle: LAST / Resolution: 1.2→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 12 229 1656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061522
X-RAY DIFFRACTIONf_angle_d1.1032067
X-RAY DIFFRACTIONf_dihedral_angle_d13.309580
X-RAY DIFFRACTIONf_chiral_restr0.067240
X-RAY DIFFRACTIONf_plane_restr0.006274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.24290.2632680.2294995X-RAY DIFFRACTION100
1.2429-1.29270.22682670.21935001X-RAY DIFFRACTION100
1.2927-1.35150.23532680.21064991X-RAY DIFFRACTION100
1.3515-1.42280.22282670.18855021X-RAY DIFFRACTION100
1.4228-1.51190.2142680.18235024X-RAY DIFFRACTION100
1.5119-1.62860.18222680.16795053X-RAY DIFFRACTION100
1.6286-1.79250.20722680.17615061X-RAY DIFFRACTION100
1.7925-2.05190.20762680.17655107X-RAY DIFFRACTION100
2.0519-2.5850.19112680.18275153X-RAY DIFFRACTION100
2.585-34.02640.18242640.19145318X-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)
10.62660.3357-0.00480.30370.09290.5182-0.03840.02720.0487-0.03330.01240.0312-0.01790.00680.0220.0461-0.0017-0.00830.03590.00790.04543.866619.171314.2864
20.86290.0632-0.39910.0084-0.02360.24140.073-0.0237-0.1329-0.0546-0.0097-0.1348-0.0580.0654-0.0190.0585-0.01850.01360.062-0.00730.084514.975123.470418.7057
30.4698-0.27170.1250.84550.65270.8355-0.0279-0.0471-0.0320.18150.04960.05780.15870.0614-0.01850.07150.00980.00430.04970.00470.0457.54121.009738.7402
40.4107-0.2855-0.09731.15970.59221.65340.03080.1901-0.01330.10820.1573-0.16740.14030.2767-0.12530.06940.0162-0.020.1287-0.02860.077616.399724.544144.0039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 284:370
2X-RAY DIFFRACTION2CHAIN C AND RESID 4:10
3X-RAY DIFFRACTION3CHAIN B AND RESID 284:370
4X-RAY DIFFRACTION4CHAIN D AND RESID 5:10

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