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

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Basic information

Entry
Database: PDB / ID: 4jog
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide V-iCAL36 (ANSRVPTSII)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • V-iCAL36 peptide
KeywordsPEPTIDE BINDING PROTEIN / PDZ / CFTR Associated Ligand / CAL / PIST / FIG / PDZ-peptide 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: 1.465 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: V-iCAL36 peptide
D: V-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1007
Polymers20,8244
Non-polymers2763
Water3,243180
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: V-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5964
Polymers10,4122
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-5 kcal/mol
Surface area5550 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: V-iCAL36 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5043
Polymers10,4122
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-6 kcal/mol
Surface area5320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.673, 47.938, 97.848
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 V-iCAL36 peptide


Mass: 1058.210 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% (w/v) polyethylene glycol (PEG), 0.2 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: 1.465→19.656 Å / Num. all: 30756 / Num. obs: 30171 / % possible obs: 98.1 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 3.05 / Rmerge(I) obs: 0.088 / Rsym value: 0.068 / Net I/σ(I): 16.71
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.465-1.540.5293.050.504188.7
1.55-1.650.285.720.3421100
1.66-1.780.1778.720.2151100
1.79-1.950.10313.650.1271100
1.96-2.180.05221.290.0781100
2.19-2.510.0426.640.061100

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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: 1.465→19.655 Å / SU ML: 0.18 / Cross valid method: Omit map / σ(F): 1.99 / σ(I): 3.05 / Phase error: 17.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 1516 5.02 %In thin shells
Rwork0.1787 ---
obs0.1794 30171 99.06 %-
all-30171 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.287 Å2 / ksol: 0.413 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.372 Å2-0 Å2-0 Å2
2---0.8709 Å2-0 Å2
3----0.5012 Å2
Refinement stepCycle: LAST / Resolution: 1.465→19.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 18 180 1636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061512
X-RAY DIFFRACTIONf_angle_d1.0422047
X-RAY DIFFRACTIONf_dihedral_angle_d14.071573
X-RAY DIFFRACTIONf_chiral_restr0.065239
X-RAY DIFFRACTIONf_plane_restr0.005269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.465-1.5170.31871480.2762573X-RAY DIFFRACTION91
1.517-1.57770.28231520.2322833X-RAY DIFFRACTION100
1.5777-1.64950.24481520.19962851X-RAY DIFFRACTION100
1.6495-1.73640.22491520.19042847X-RAY DIFFRACTION100
1.7364-1.84510.21111520.16832870X-RAY DIFFRACTION100
1.8451-1.98740.18241520.15792858X-RAY DIFFRACTION100
1.9874-2.18720.1731520.1632902X-RAY DIFFRACTION100
2.1872-2.50310.18031520.17112904X-RAY DIFFRACTION100
2.5031-3.15160.20341520.1812934X-RAY DIFFRACTION100
3.1516-19.65650.16181520.17123083X-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)
10.3677-0.24430.13380.4669-0.01150.3789-0.0266-0.0350.04060.04420.0090.00360.0233-0.0050.01620.06770.00040.00160.0682-0.00760.061832.729919.534783.6067
20.3829-0.22270.40210.7408-0.45430.50610.04310.0015-0.0318-0.1605-0.0191-0.0140.0521-0.04-0.02030.08750.00390.00080.07010.00170.05462921.057359.4596
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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