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

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Basic information

Entry
Database: PDB / ID: 4nmr
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36(Ac-K-5) (ANSR[Ac-K]PTSII)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36(Ac-K-5) peptide
Keywordsprotein transport/inhibitor / CAL / PIST / GOPC / FIG / CFTR / PDZ / 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 / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / 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 / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / 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 / 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-5) peptide / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.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: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(Ac-K-5) peptide
D: iCAL36(Ac-K-5) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0585
Polymers20,9664
Non-polymers921
Water4,774265
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: iCAL36(Ac-K-5) peptide


Theoretical massNumber of molelcules
Total (without water)10,4832
Polymers10,4832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-5 kcal/mol
Surface area5780 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: iCAL36(Ac-K-5) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5753
Polymers10,4832
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area4970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.137, 47.514, 100.536
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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9HD26
#2: Protein/peptide iCAL36(Ac-K-5) peptide


Type: Oligopeptide / Class: Inhibitor / Mass: 1129.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: peptide synthesis / References: iCAL36(Ac-K-5) peptide
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Details: peptide synthesis
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 31% (w/v) polyethylene glycol (PEG), 0.15 M sodium chloride, 0.1 M tris(hydroxymethyl)aminomethane (Tris) pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K

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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: 1.55→19.5 Å / Num. all: 25914 / Num. obs: 25713 / % possible obs: 99.2 % / Observed criterion σ(F): 8 / Observed criterion σ(I): 23.85 / Rsym value: 0.08 / Net I/σ(I): 23.85
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.55-1.63.7327380.509196.6
1.61-1.715.9241090.427198.7
1.72-1.859.57389026.6199.6
1.86-2.0316.65359115.8199.8
2.04-2.2625.58311710.3199.8
2.27-2.6133.4628857.6199.9

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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: 4E34 chain A

4e34


Resolution: 1.55→19.475 Å / SU ML: 0.15 / Cross valid method: presence of peptide density / σ(F): 1.99 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1310 5.1 %In thin shells
Rwork0.1878 ---
obs0.1894 25711 99.29 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.642 Å2 / ksol: 0.411 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6279 Å2-0 Å2-0 Å2
2---2.3604 Å2-0 Å2
3----0.2674 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 6 265 1713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061467
X-RAY DIFFRACTIONf_angle_d1.061979
X-RAY DIFFRACTIONf_dihedral_angle_d13.079552
X-RAY DIFFRACTIONf_chiral_restr0.065232
X-RAY DIFFRACTIONf_plane_restr0.005256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.6120.28211260.23062603X-RAY DIFFRACTION97
1.612-1.68540.27381300.23382649X-RAY DIFFRACTION99
1.6854-1.77420.26821970.2072625X-RAY DIFFRACTION99
1.7742-1.88520.2121310.1952711X-RAY DIFFRACTION100
1.8852-2.03070.21911320.18212693X-RAY DIFFRACTION100
2.0307-2.23480.2251320.18382727X-RAY DIFFRACTION100
2.2348-2.55750.23571320.20232745X-RAY DIFFRACTION100
2.5575-3.21980.20541980.18092719X-RAY DIFFRACTION100
3.2198-19.47680.17551320.16542929X-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)
10.06390.02820.01630.02530.02020.04630.00710.0128-0.00730.0128-0.0059-0.0102-0.01980.03640.00140.0408-0.00340.00740.0280.00530.03835.997118.881715.6999
20.07850.03480.03150.07890.05170.03530.0322-0.0219-0.0220.0752-0.0129-0.01480.02620.0135-0.00630.04980.00470.00360.04310.00140.03055.455821.085139.9878
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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