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

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Basic information

Entry
Database: PDB / ID: 4jok
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide Y-iCAL36 (ANSRYPTSII)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • Y-iCAL36 peptide
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 / 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: 1.09 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

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: Y-iCAL36 peptide
D: Y-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2287
Polymers20,9524
Non-polymers2763
Water3,963220
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: Y-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6604
Polymers10,4762
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-5 kcal/mol
Surface area5450 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: Y-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5683
Polymers10,4762
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-7 kcal/mol
Surface area5080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.167, 47.824, 97.461
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 Y-iCAL36 peptide


Mass: 1122.253 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 38.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 34% (w/v) polyethylene glycol (PEG), 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: 1.09→18.46 Å / Num. all: 71374 / Num. obs: 70086 / % possible obs: 98.2 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 4.98 / Rmerge(I) obs: 0.083 / Rsym value: 0.075 / Net I/σ(I): 15.57
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.09-1.150.3484.980.345192.4
1.16-1.230.2257.030.2631100
1.24-1.320.1619.070.1931100
1.33-1.450.10512.380.1351100
1.46-1.620.06417.530.0921100
1.63-1.870.04223.290.0671100

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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: 1.09→18.46 Å / SU ML: 0.12 / Cross valid method: Omit map / σ(F): 1.99 / σ(I): 4.98 / Phase error: 15.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 3525 5.03 %In thin shells
Rwork0.1806 ---
obs0.182 70084 98.23 %-
all-70086 --
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.367 Å2 / ksol: 0.504 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.922 Å2-0 Å2-0 Å2
2---0.9481 Å2-0 Å2
3----0.9738 Å2
Refinement stepCycle: LAST / Resolution: 1.09→18.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 18 220 1677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051565
X-RAY DIFFRACTIONf_angle_d1.0732124
X-RAY DIFFRACTIONf_dihedral_angle_d14.78601
X-RAY DIFFRACTIONf_chiral_restr0.069240
X-RAY DIFFRACTIONf_plane_restr0.006285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.1290.22563190.2235819X-RAY DIFFRACTION87
1.129-1.17420.22743570.19126684X-RAY DIFFRACTION100
1.1742-1.22760.18913580.18196677X-RAY DIFFRACTION100
1.2276-1.29230.1743580.17196724X-RAY DIFFRACTION100
1.2923-1.37330.18413580.16886694X-RAY DIFFRACTION100
1.3733-1.47920.17923580.16146723X-RAY DIFFRACTION100
1.4792-1.6280.17043580.15736774X-RAY DIFFRACTION100
1.628-1.86340.18443580.16676800X-RAY DIFFRACTION100
1.8634-2.34690.17833580.17516862X-RAY DIFFRACTION100
2.3469-18.46260.18363430.19776802X-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)
10.58940.30120.09910.56360.1060.5295-0.03640.03980.0401-0.07180.0240.0282-0.01970.01150.01270.0442-0.004-0.00350.03960.00760.04343.814519.708214.2975
20.49610.03090.41640.95180.54020.96730.031-0.0366-0.02990.16270.00110.02650.13940.0169-0.02680.07080.0010.00040.05370.00470.0467.399720.964138.5715
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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