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

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Basic information

Entry
Database: PDB / ID: 4nmp
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(Ac-K-3) (ANSRWP[Ac-K]SII)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36(Ac-K-3) peptide
Keywordsprotein transport/inhibitor / CAL / GOPC / PIST / FIG / PDZ domain / PDZ-peptide complex / CFTR / CFTR associated ligand / 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 / 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
iCAL36(Ac-K-3) peptide / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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(Ac-K-3) peptide
D: iCAL36(Ac-K-3) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3206
Polymers21,1364
Non-polymers1842
Water3,801211
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(Ac-K-3) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6603
Polymers10,5682
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-7 kcal/mol
Surface area5170 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: iCAL36(Ac-K-3) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6603
Polymers10,5682
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-7 kcal/mol
Surface area5370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.924, 47.659, 97.161
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 / 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(Ac-K-3) peptide


Type: Oligopeptide / Class: Inhibitor / Mass: 1214.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: iCAL36(Ac-K-3) peptide
#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.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 34% (w/v) polyethylene glycol (PEG) 3350, 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: 1.3→19.5 Å / Num. all: 41906 / Num. obs: 41733 / % possible obs: 99.6 % / Observed criterion σ(F): 8.4 / Observed criterion σ(I): 29.31 / Rsym value: 0.084 / Net I/σ(I): 29.31
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.3-1.374.9366770.672198.7
1.38-1.466.99590848.4199.5
1.47-1.5810.49601132199.6
1.59-1.7316.4535520.1199.9
1.74-1.9326.22485911.7199.9
1.94-2.2346.0344426.21100

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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: 1.3→19.456 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 16.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 2094 5.02 %In thin shells
Rwork0.1807 ---
obs0.1818 41732 99.63 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.698 Å2 / ksol: 0.449 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1005 Å2-0 Å2-0 Å2
2---0.7255 Å2-0 Å2
3----0.375 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 12 211 1679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061550
X-RAY DIFFRACTIONf_angle_d1.0762100
X-RAY DIFFRACTIONf_dihedral_angle_d14.488585
X-RAY DIFFRACTIONf_chiral_restr0.07236
X-RAY DIFFRACTIONf_plane_restr0.005275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33030.27641050.25812605X-RAY DIFFRACTION98
1.3303-1.36350.23162050.2232503X-RAY DIFFRACTION99
1.3635-1.40040.22511050.20082630X-RAY DIFFRACTION100
1.4004-1.44160.20091050.19042644X-RAY DIFFRACTION100
1.4416-1.48810.20992090.17812527X-RAY DIFFRACTION99
1.4881-1.54120.20831050.1652635X-RAY DIFFRACTION100
1.5412-1.60290.1921050.16722640X-RAY DIFFRACTION100
1.6029-1.67580.19822010.16072569X-RAY DIFFRACTION100
1.6758-1.76410.21781140.16922669X-RAY DIFFRACTION100
1.7641-1.87460.1941050.17052677X-RAY DIFFRACTION100
1.8746-2.01920.20271730.16572608X-RAY DIFFRACTION100
2.0192-2.22210.18571420.17542670X-RAY DIFFRACTION100
2.2221-2.54310.21811050.18012723X-RAY DIFFRACTION100
2.5431-3.20170.21432100.18822646X-RAY DIFFRACTION100
3.2017-19.45780.15411050.18122892X-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)
10.17890.02410.18070.2707-0.01560.4145-0.00120.01150.0229-0.028-0.00980.002-0.00820.02050.00360.0393-0.0055-0.00210.03340.0040.03793.661119.649314.1224
20.32420.13540.38770.44890.24940.50810.0466-0.0241-0.00360.0974-0.01530.00420.0744-0.00820.00780.0457-0.00460.00030.03220.00040.02947.575720.99438.3024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 284:370 )A284 - 370
2X-RAY DIFFRACTION2( CHAIN B AND RESID 284:370 )B284 - 370

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