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

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Basic information

Entry
Database: PDB / ID: 4nmv
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(BRB-K-1) (ANSRWPTS[4-bromobenzoic-acyl-K]I)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36(BRB-K-1) peptide
Keywordsprotein transport/inhibitor / CAL / GOPC / PIST / FIG / CFTR / PDZ / PDZ-peptide / protein transport-inhibitor 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
iCAL36(BRB-K-1) peptide / 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: Plos One / Year: 2014
Title: Chemically Modified Peptide Scaffolds Target the CFTR-Associated Ligand PDZ Domain.
Authors: Amacher, J.F. / Zhao, R. / Spaller, M.R. / Madden, D.R.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: iCAL36(BRB-K-1) peptide
D: iCAL36(BRB-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5786
Polymers21,3944
Non-polymers1842
Water3,657203
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(BRB-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7893
Polymers10,6972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-7 kcal/mol
Surface area5260 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: iCAL36(BRB-K-1) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7893
Polymers10,6972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-5 kcal/mol
Surface area5320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.986, 47.944, 97.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCAL PDZ domain bound to decameric peptide

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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: 9353.722 Da / Num. of mol.: 2 / Fragment: 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 iCAL36(BRB-K-1) peptide


Type: Oligopeptide / Class: Inhibitor / Mass: 1343.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: iCAL36(BRB-K-1) peptide
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 31% (w/v) polyethylene glycol (PEG), 0.1 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: 0.8856 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 18, 2011
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.4→19.5 Å / Num. all: 34036 / Num. obs: 33913 / % possible obs: 99.6 % / Observed criterion σ(F): 7.8 / Observed criterion σ(I): 25.63
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.4-1.464.2945400.686199.1
1.47-1.586.5860740.437199.4
1.59-1.7310.8254570.256199.6
1.74-1.9418.93508214199.9
1.95-2.2334.3643027.31100
2.24-2.7345.4637935.11100

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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→19.5 Å / SU ML: 0.19 / Cross valid method: omit peptide density / σ(F): 2 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 1720 5.07 %In thin shells
Rwork0.1823 ---
obs0.1833 33913 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.489 Å2 / ksol: 0.428 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3457 Å20 Å20 Å2
2---0.6878 Å20 Å2
3----0.6578 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 12 203 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081533
X-RAY DIFFRACTIONf_angle_d1.1392073
X-RAY DIFFRACTIONf_dihedral_angle_d15.843574
X-RAY DIFFRACTIONf_chiral_restr0.071234
X-RAY DIFFRACTIONf_plane_restr0.006268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.44120.28551720.24422590X-RAY DIFFRACTION99
1.4412-1.48770.242860.21862692X-RAY DIFFRACTION99
1.4877-1.54090.21721720.19652584X-RAY DIFFRACTION99
1.5409-1.60250.1991720.1882605X-RAY DIFFRACTION99
1.6025-1.67540.2032860.17482685X-RAY DIFFRACTION100
1.6754-1.76370.20511720.17842658X-RAY DIFFRACTION100
1.7637-1.87410.20621450.16932668X-RAY DIFFRACTION100
1.8741-2.01870.19841130.16422699X-RAY DIFFRACTION100
2.0187-2.22160.17971720.17532662X-RAY DIFFRACTION100
2.2216-2.54250.1961390.18462718X-RAY DIFFRACTION100
2.5425-3.2010.19361190.17872780X-RAY DIFFRACTION100
3.201-19.54720.19871720.1822852X-RAY DIFFRACTION100

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