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- PDB-4k78: CFTR Associated Ligand (CAL) E317A PDZ domain bound to peptide iC... -

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Basic information

Entry
Database: PDB / ID: 4k78
TitleCFTR Associated Ligand (CAL) E317A PDZ domain bound to peptide iCAL36-QDTRL (ANSRWQDTRL)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36-QDTRL peptide
KeywordsPEPTIDE BINDING PROTEIN/PROTEIN BINDING / PDZ domain / CAL / PIST / FIG / PDZ-peptide complex / CFTR Associated Ligand / CFTR / PEPTIDE BINDING PROTEIN-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 / 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: 1.8 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
DepositionApr 16, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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: iCAL36-QDTRL peptide


Theoretical massNumber of molelcules
Total (without water)10,6242
Polymers10,6242
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-3 kcal/mol
Surface area5420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.821, 61.821, 97.446
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-407-

HOH

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Components

#1: Protein Golgi-associated PDZ and coiled-coil motif-containing protein / CFTR-associated ligand / Fused in glioblastoma / PDZ protein interacting specifically with TC10 / PIST


Mass: 9375.748 Da / Num. of mol.: 1 / Fragment: PDZ domain / Mutation: E317A
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 iCAL36-QDTRL peptide


Mass: 1248.349 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40% (w/v) polyethylene glycol (PEG), 0.9 M sodium thiosulfate pentahydrate, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 8, 2013
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→19.133 Å / Num. all: 10797 / Num. obs: 10781 / % possible obs: 99.9 % / Observed criterion σ(F): 2.04 / Observed criterion σ(I): 6.53 / Rsym value: 0.11 / Net I/σ(I): 26.01
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.8-1.856.5398261.71100
1.86-1.9810.3174745.71100
1.99-2.1316.44152626.81100
2.14-2.3421.94153518.21100
2.35-2.6125.48134214.61100
2.62-3.0133.8212189.31100

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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 (CAL PDZ bound to iCAL36 peptide)

4e34


Resolution: 1.8→19.133 Å / SU ML: 0.19 / Cross valid method: Omit map / σ(F): 2.04 / σ(I): 6.53 / Phase error: 17.02 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 560 5.19 %In thin shells
Rwork0.1832 ---
obs0.1851 10780 100 %-
all-10781 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.834 Å2 / ksol: 0.497 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1969 Å2-0 Å2-0 Å2
2--1.1969 Å2-0 Å2
3----2.3939 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 0 0 69 814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008786
X-RAY DIFFRACTIONf_angle_d1.2031066
X-RAY DIFFRACTIONf_dihedral_angle_d15.776293
X-RAY DIFFRACTIONf_chiral_restr0.086120
X-RAY DIFFRACTIONf_plane_restr0.005142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.9810.21451400.17412475X-RAY DIFFRACTION100
1.981-2.26720.22041400.15162499X-RAY DIFFRACTION100
2.2672-2.8550.21451400.17662529X-RAY DIFFRACTION100
2.855-19.13450.22631400.20222717X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.5397 Å / Origin y: 23.4476 Å / Origin z: 36.7985 Å
111213212223313233
T0.0537 Å2-0.002 Å2-0.0156 Å2-0.0563 Å20.0106 Å2--0.0549 Å2
L0.2044 °2-0.1454 °20.033 °2-0.4489 °2-0.1586 °2--0.4009 °2
S0.0284 Å °-0.0587 Å °-0.0692 Å °0.033 Å °0.0204 Å °-0.0612 Å °0.0709 Å °0.0063 Å °-0.0006 Å °
Refinement TLS groupSelection details: CHAIN A AND RESID 284:370

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